diff --git a/data/nextstrain/hmpv/all-clades/NC_039199/pathogen.json b/data/nextstrain/hmpv/all-clades/NC_039199/pathogen.json index eade4628..15d7cab7 100644 --- a/data/nextstrain/hmpv/all-clades/NC_039199/pathogen.json +++ b/data/nextstrain/hmpv/all-clades/NC_039199/pathogen.json @@ -14,12 +14,12 @@ "minMatchLength": 20, "allowedMismatches": 10, "windowSize": 30 -}, + }, "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" }, - "defaultCds": "F", + "defaultCds": "G", "files": { "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", @@ -52,16 +52,22 @@ "mixedSitesThreshold": 10 }, "frameShifts": { - "enabled": true - }, - "stopCodons": { - "enabled": false, - "ignoredStopCodons": [ + "enabled": true, + "scoreWeight": 20, + "ignoreFrameShifts": [ { - "codon": 320, + "codonRange": { + "begin": 206, + "end": 224 + }, "cdsName": "G" } ] + }, + "stopCodons": { + "enabled": true, + "ignoredStopCodons": [], + "scoreWeight": 5 } }, "shortcuts": [ @@ -82,4 +88,4 @@ "G", "L" ] -} +} \ No newline at end of file diff --git a/data/nextstrain/hmpv/all-clades/NC_039199/tree.json b/data/nextstrain/hmpv/all-clades/NC_039199/tree.json index de3bcb24..49f5a1f6 100644 --- a/data/nextstrain/hmpv/all-clades/NC_039199/tree.json +++ b/data/nextstrain/hmpv/all-clades/NC_039199/tree.json @@ -155,18 +155,6 @@ "latitude": 0.0236, "longitude": 37.9062 }, - "USA": { - "latitude": 38.916963, - "longitude": -98.891372 - }, - "Peru": { - "latitude": -9.650468, - "longitude": -75.328211 - }, - "Vietnam": { - "latitude": 16.16667, - "longitude": 107.83333 - }, "Australia": { "latitude": -24.7761085, "longitude": 134.755 @@ -178,6 +166,18 @@ "Russia": { "latitude": 64.6863136, "longitude": 97.7453061 + }, + "Vietnam": { + "latitude": 16.16667, + "longitude": 107.83333 + }, + "Peru": { + "latitude": -9.650468, + "longitude": -75.328211 + }, + "USA": { + "latitude": 38.916963, + "longitude": -98.891372 } } }, @@ -188,6 +188,10 @@ "latitude": 35.000074, "longitude": 104.999927 }, + "South America": { + "latitude": -13.083583, + "longitude": -58.470721 + }, "Europe": { "latitude": 49.646237, "longitude": 10.799454 @@ -200,10 +204,6 @@ "latitude": 28.2367447, "longitude": -97.738017 }, - "South America": { - "latitude": -13.083583, - "longitude": -58.470721 - }, "Oceania": { "latitude": -25.0562891, "longitude": 152.008576 @@ -229,31 +229,39 @@ "mutations": { "nuc": [ "G11A", - "A12G", + "A20C", "T26C", + "G34A", + "G36A", + "G63A", "T70C", + "C78T", "G81A", "G126A", - "T129C", - "A132G", - "G195A", + "A132C", + "A189G", + "G195T", "G208A", "C213T", + "T225C", + "A231G", "A250T", + "A255G", "T259C", + "G270A", "G276A", - "G279A", - "G288A", "G291A", - "C309T", - "A312G", + "C300T", + "T314C", "C318T", - "G326A", + "T319C", "G330A", "C337T", + "G339A", "A346G", - "A363G", + "A356G", "T369G", + "A372G", "C384T", "C390T", "G393A", @@ -261,434 +269,455 @@ "G399A", "C405T", "G417A", - "A429G", "G435A", - "C446T", "C450T", - "T456C", - "T474C", - "C477T", - "T486C", + "T486-", "C495T", - "C519T", + "C513T", "C546T", - "C564A", + "T549C", "G573T", - "C577T", "C585T", "C591T", "G597A", "C604A", - "T606-", "G627A", - "A639G", "A640G", "G642A", "G654A", + "T657C", "C660T", - "G662A", - "C666T", "T676C", + "A684G", "C697T", - "A729T", - "T744A", - "C750A", + "G708A", + "C723-", + "A741-", + "T744-", + "C750-", "C766T", - "C783T", + "T774A", "G798A", - "C801T", "G825T", "G837A", "C843T", - "T849C", - "T856C", - "A861G", "C870T", - "A876-", + "C873G", "G882A", - "A885G", + "C894T", "A900G", "C927T", "A939G", - "T942C", + "T948-", "T949C", - "G954A", "C960T", - "T969-", + "T969A", + "A981G", + "C982T", "C990T", "A1020C", - "A1041T", + "C1026T", + "C1032T", + "T1047A", "C1054A", - "A1065G", + "A1077G", "T1078C", - "A1086T", "T1092A", + "A1106G", + "T1110C", + "A1119T", "A1131C", "T1134C", - "C1137T", "T1140C", - "T1152C", + "A1149G", "G1164A", "G1170A", "T1182C", "T1191C", - "G1192A", - "G1233C", - "A1253T", + "C1200T", + "G1205A", + "A1210G", + "G1233T", "T1274C", - "T1277G", "T1302A", "T1326C", - "C1335T", - "G1338A", "T1343C", - "T1350A", - "A1362G", "A1367G", - "G1376A", "T1379C", "G1383A", - "A1394-", + "A1394T", "T1395C", - "T1401C", + "G1397A", + "T1409C", + "T1415C", "G1417A", - "A1426G", - "A1431T", + "G1422A", + "A1425C", + "C1428T", "T1435C", "C1438T", - "C1441T", + "T1440C", + "A1445G", "G1451A", - "A1454G", + "A1461G", "T1466C", "A1469C", - "T1472C", - "A1478G", - "C1480T", - "A1489C", + "T1487C", + "G1488A", "A1491G", + "T1492A", "G1496A", - "T1504-", - "G1509A", - "T1513C", + "G1500A", + "T1504C", + "C1511T", + "G1514A", "C1520T", - "A1521G", + "A1532G", "C1537T", "C1541T", "G1544A", "G1553A", + "C1554T", + "T1555C", "A1556G", + "A1574G", "C1577T", "A1586G", + "G1589A", "C1593T", - "T1594C", "G1595A", - "C1599T", + "A1601T", "T1607C", "C1610T", "A1611G", - "C1612T", "C1613T", "G1622A", "C1635T", - "T1655C", - "A1658C", + "A1658T", "G1664A", "A1667G", - "T1682C", + "T1676C", "T1694C", "A1700G", "T1718C", - "T1748-", + "A1739G", + "T1748A", + "T1755C", "G1766A", - "A1772T", + "C1769T", "T1773C", "G1775A", - "G1787A", - "A1814G", - "A1817T", - "A1818C", - "C1826T", + "A1793G", + "A1817C", + "A1820T", "T1835A", - "A1857C", - "T1862C", + "A1853T", "G1865A", + "C1886T", "G1887A", - "C1910G", + "T1899C", + "C1910A", + "T1925C", "A1928G", "G1931A", - "A1958G", + "A1940C", "G1963A", - "C1968A", - "A1970G", + "T1985C", "T1998C", "A2003C", "A2006G", "A2009G", + "A2015G", "C2021T", - "A2054T", - "C2060A", - "C2086T", - "T2096C", - "A2161C", + "T2039C", + "C2060T", + "A2087T", + "A2090G", + "C2093T", + "G2098A", + "A2104G", + "T2108A", + "T2126C", "A2164G", "C2176T", "C2188T", - "T2203C", "A2212T", "A2230G", "A2231G", "G2239A", + "C2243T", "G2245A", "T2246C", - "C2272T", - "G2278A", + "A2260G", + "A2302G", "G2305T", "C2306T", "C2326T", "C2327T", - "C2338T", - "A2404C", + "A2359G", + "A2377G", + "A2401C", "T2428C", "G2440A", "C2452T", "T2461C", - "C2468T", - "G2470A", - "C2483T", - "C2491T", + "A2482G", + "C2485A", + "A2488G", + "T2494C", "A2497G", "A2500T", "A2515G", - "C2557T", + "C2533T", + "A2542G", "A2581G", "C2596T", "A2602G", - "A2623G", + "T2611C", + "T2617C", "G2626A", - "C2629T", - "C2631T", - "C2656A", + "T2638G", + "C2656T", "A2659G", "T2689C", "T2704A", - "A2719C", - "A2731G", - "G2737A", - "T2752C", "G2758A", "T2762C", + "A2764G", "T2779C", "C2791A", "C2797T", "A2806G", - "T2812-", + "C2810T", "G2821A", "T2824A", - "C2830T", - "A2845G", - "T2860C", - "C2872T", + "C2830G", + "C2854T", + "A2863G", + "A2869C", + "A2874G", "A2875G", - "A2878T", + "A2878C", "C2886G", "T2887C", + "C2893T", "T2896C", + "G2902A", "T2911C", - "C2914A", + "C2914G", "T2915C", - "G2917-", + "G2917A", "G2920A", + "C2930A", "C2934-", - "G2937T", - "G2945A", - "G2950T", + "C2938T", + "G2944A", + "C2946T", "G2952A", "C2953T", - "C2960T", - "C2961A", - "T2963A", - "C2966T", + "A2955G", + "C2961T", + "T2963C", + "T2965C", "T2967C", "C2968T", "T2970A", - "G2972A", "C2975T", "T2977A", - "A2978T", "C2983T", "C2985T", - "C2990T", - "C3016T", + "C2986T", + "G3009-", "A3017T", - "T3022A", + "T3023G", "A3025C", "C3032A", - "A3033G", "A3037G", - "T3075C", - "T3076-", + "G3067A", "G3084A", - "T3085C", + "T3085A", "A3087C", "T3096C", - "T3108G", + "A3099G", + "T3108A", "C3117T", + "C3120T", "G3129A", + "C3138T", + "C3166T", "G3171A", "T3189C", "C3199T", - "G3201A", + "G3204A", + "A3207G", "C3210T", - "G3232A", + "A3216T", + "G3219A", "C3234T", "C3243T", - "A3252-", - "T3262C", + "A3252C", + "A3264T", "G3270A", + "T3279C", "A3282T", "G3291A", "G3296A", "C3316T", "G3318A", + "G3330A", "A3339G", + "A3357G", "C3360T", "T3363C", - "A3369T", - "A3378T", + "A3390C", "T3393A", - "T3414C", - "T3423-", + "T3405C", + "G3415A", "C3435A", - "A3453C", + "C3436A", + "A3444G", + "A3453G", "C3455A", "G3465A", + "A3466G", "C3471T", - "T3498C", + "T3498-", "G3507A", "T3516G", "T3519G", - "T3523C", + "G3522C", "G3525A", - "A3528C", "T3552A", + "G3564A", "C3568T", + "A3570G", "A3573T", "C3574A", - "T3576C", + "A3588G", "G3594A", - "C3597T", "C3605A", - "C3621T", - "G3648A", + "C3609T", + "T3624C", "C3651T", + "A3669G", "C3681T", "T3684A", + "A3687G", "T3705A", "T3712C", + "A3720T", + "A3729G", + "C3730T", + "A3732G", + "T3741C", "T3744A", "C3747A", - "A3748T", - "A3804G", - "A3807G", "A3813G", + "G3816A", "T3823A", "A3834G", "T3837C", - "G3864C", + "C3840T", + "A3852G", + "G3864T", "A3867G", "G3882C", + "T3885C", "C3891T", + "G3894A", + "C3900T", + "A3909T", "T3921C", "T3927C", "G3932A", - "G3939A", + "G3939C", + "C3945T", "T3958C", - "A3966G", "C3969T", "A3975G", - "C3985A", - "A3987G", - "A3999C", + "G3996A", "T4029C", - "C4050T", - "C4056T", + "A4041T", + "C4044T", "A4071G", - "T4077C", "G4089A", "G4095A", - "G4098A", "A4107C", + "T4116C", "T4122C", "T4125C", "T4140C", + "T4155C", "T4179A", "T4185C", "G4188T", - "T4197A", + "T4197G", "G4209A", "A4212G", - "G4215-", + "G4215A", + "C4224G", "C4236T", - "A4237C", - "A4242T", + "G4245A", "G4254A", "G4260A", - "A4261C", - "T4275A", + "A4262C", + "C4263T", "T4278C", - "A4290G", + "C4299T", "A4302T", - "G4305A", - "A4311-", + "A4323G", "C4326T", + "G4329A", "A4344G", "C4347T", - "T4359-", + "T4359A", "A4368G", "G4371A", - "G4377A", + "C4386T", "C4392T", - "G4396A", "A4400G", "A4410G", "A4416G", "A4428G", - "C4434T", + "T4440C", "C4443T", - "G4448A", - "G4455A", - "T4461C", - "C4467-", + "G4446A", + "C4467A", "T4468C", "G4473A", - "A4482G", "G4487A", "C4491T", "G4496A", - "A4512G", + "G4506A", "C4521T", "C4527T", - "A4543G", + "C4540T", + "C4551T", "C4557T", + "T4560A", "C4562G", "C4569T", "T4578C", "G4579A", "T4581C", - "T4582A", + "T4582C", "T4584C", "A4593C", - "C4611A", - "A4617G", + "A4604G", + "A4608G", + "A4614-", "G4634A", - "C4641T", - "A4648G", + "A4644C", "T4650C", + "C4653T", "T4665C", "A4667G", "T4683A", - "G4687-", + "A4685-", + "A4686-", + "G4687A", "T4688C", + "A4690-", "T4692-", "T4693-", "A4694-", @@ -699,7 +728,7 @@ "A4699-", "A4700-", "A4701-", - "T4702A", + "T4702-", "T4703-", "A4704-", "A4705-", @@ -717,555 +746,573 @@ "A4717-", "A4718-", "A4719-", - "T4722C", + "A4720-", + "T4721A", + "T4722-", "C4745T", - "G4748A", "G4754A", + "A4760-", + "T4784C", "T4805C", - "A4844G", + "A4829T", + "C4838T", "A4845T", "T4860C", - "A4862C", "A4865G", "A4871G", - "A4892G", + "G4880A", + "G4891A", + "C4901T", "A4904G", - "A4919C", + "A4919T", "C4925T", "G4937A", "A4940G", "T4946C", "C4952T", - "C4953T", - "T4979G", + "A4955C", + "T4979A", "T4982C", - "T4988C", + "T4991C", "C4994T", "A4998G", "C5000A", "A5009G", + "C5018T", "T5021C", - "C5024T", + "T5033C", "T5036C", "A5045G", "G5058A", "T5060A", "G5069A", + "A5087G", "A5090T", "A5108G", + "A5111G", + "T5114C", + "A5123G", "G5124A", + "C5126A", "C5127T", "T5132C", + "T5162C", "T5163C", - "T5174C", - "C5177A", + "C5177T", "G5182A", - "G5186A", "G5189A", "G5195A", "G5216A", + "C5217T", "C5219G", "C5228T", + "T5240A", "A5246C", - "T5265C", - "G5299A", - "A5310C", - "T5313C", - "T5322C", + "T5253C", + "A5310T", + "G5311A", + "T5312A", + "T5313A", "C5337T", + "T5349A", "G5355A", "C5358A", "G5368A", - "T5370A", "T5371C", "A5373G", - "G5391A", + "T5394A", + "T5397C", + "T5400C", "A5411G", + "T5436A", "G5448A", + "C5470A", "C5472A", - "T5474A", "C5475T", - "T5498A", + "G5479A", + "T5514A", "T5529C", "A5533G", "C5543A", - "C5568A", - "T5574A", + "T5562A", + "T5574G", "T5591C", - "T5595A", - "T5599C", + "G5598A", + "A5601G", "A5607G", - "T5610C", + "C5614T", "A5616G", "C5623T", + "C5637T", "C5640T", - "C5643T", + "T5646C", + "T5649C", "G5658A", "C5668T", - "A5673G", - "C5679T", + "A5674G", + "G5682A", + "C5684T", "C5690A", - "T5713A", + "T5710A", + "T5713C", "C5714A", - "A5715G", "C5717T", "G5731A", - "T5732C", "C5733A", - "C5738T", "A5741G", - "G5742A", + "A5743C", "T5745C", - "A5751T", "A5752G", "A5756T", - "T5757C", "G5758A", - "A5761G", "C5763A", "A5764G", - "C5765T", + "T5775G", "T5781G", - "G5793A", + "T5782C", + "G5792A", + "T5796C", "A5800G", - "C5802T", + "C5802-", "C5804T", "C5807T", "A5808C", - "G5816A", "T5817A", "C5820T", - "A5823C", + "C5826T", "A5831G", + "A5836C", "G5840A", - "A5841G", - "C5864T", - "A5871G", - "T5874C", + "C5861A", "A5884G", + "T5889C", "G5890A", - "A5891T", + "A5891C", "G5893A", "C5895T", "A5896T", - "C5903T", - "C5904T", + "A5900C", "A5906C", "A5908G", - "T5916G", "A5917G", + "A5918-", "G5922A", - "C5940A", - "A5943G", + "A5927C", + "A5935G", + "G5936A", "C5944T", "C5950T", - "A5955T", + "A5952C", + "G5953A", "T5957C", "T5958A", "G5960A", "G5962A", - "T5963C", + "T5963A", "G5964A", "C5968A", - "A5969G", - "C5970T", + "T5972C", "T5975C", - "C5982T", + "T5985C", "A5989C", - "T5992C", + "C5994T", "G5998A", "T5999C", "A6001G", "A6007G", "A6008G", - "C6012T", "C6016T", - "T6019C", - "A6020T", + "A6020C", + "C6021T", "C6022T", - "C6023A", - "A6025-", - "C6026-", - "C6027A", - "A6029-", + "C6023T", + "C6026T", + "C6027-", + "T6030-", "G6031A", - "C6036A", + "C6036T", "A6038G", - "T6040C", + "A6039G", "C6042T", - "T6047C", + "A6044T", "G6048A", "C6053A", "C6055T", - "T6060A", - "G6063A", - "A6065T", - "A6074G", + "G6064A", + "A6065C", "G6079A", + "G6083A", "T6085C", - "A6088G", "C6089T", "A6091G", + "T6108C", + "A6109-", "T6110-", - "T6111-", + "T6112C", + "G6114A", + "A6117T", "C6119T", - "A6120T", "A6121G", "G6122T", "T6123C", - "A6124T", "T6127A", - "T6128C", - "C6130T", "T6131C", + "T6133C", "T6136C", "A6142G", - "A6145G", - "A6151T", - "A6158G", - "T6160-", + "A6151C", + "T6153C", + "T6160C", "T6164A", "C6166T", + "T6167C", + "T6168A", "T6171C", "T6174C", - "C6175T", "A6176G", "C6178T", - "C6183A", + "A6179G", + "C6183-", + "A6184C", "T6186C", + "T6189C", "G6191A", - "A6192T", - "C6196-", "C6201T", "T6202C", "T6204C", - "C6206G", + "C6206T", "A6208G", + "A6212-", + "A6213-", "A6215-", - "T6228-", - "C6231A", - "A6243G", + "G6217A", + "T6228G", + "C6231T", "T6245C", "G6255A", - "A6257G", "A6274G", "T6282C", - "C6286T", - "G6296A", - "A6297G", "G6298A", "A6300G", - "T6306C", "G6310A", "G6312A", - "G6313A", - "C6316-", + "C6314G", 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"T6550C", + "C6556T", + "T6557C", "T6559C", + "A6560T", "T6562G", "T6563C", - "T6564A", - "G6568A", - "C6575A", + "T6564C", + "A6573G", + "C6575-", "A6576G", + "A6577G", + "T6580C", "C6581A", - "A6582T", + "A6582C", + "C6583-", "C6584T", "G6586C", "G6588C", - "A6594G", - "A6598G", + "A6593G", + "C6595A", "A6600T", - "T6601C", - "T6612C", "A6619G", + "A6620C", "C6621T", "G6623C", - "C6626-", - "C6628-", + "C6626T", "C6629A", - "T6631A", "T6632C", - "T6635C", + "G6634A", "C6636A", "C6641A", - "C6643T", - "C6653T", + "A6644T", + "C6650T", + "C6653A", "A6654G", "C6656T", "A6657G", "C6660T", "G6661T", - "C6662G", - "A6664-", - "G6665C", "A6670G", "C6671A", - "A6678C", "G6680C", - "T6681A", + "T6681C", "C6683A", "G6685A", + "C6691A", + "A6694G", "C6695A", "A6696G", "A6698G", - "G6711T", + "A6712G", "G6716C", "C6717A", - "T6718G", - "T6720A", - "G6722A", + "T6718A", + "T6720C", "C6725A", "C6727G", "T6729A", "T6730A", "T6732C", - "C6733A", - "A6735C", - "G6741C", "G6747A", "A6750G", "G6752C", - "G6753T", + "G6753C", "A6754G", "G6756A", + "C6758T", "A6759C", "G6761A", - "C6770A", + "G6764C", + "A6766G", "T6774C", "C6775A", "C6778A", "A6781C", - "C6782A", + "C6782-", "A6783G", + "G6785C", "C6791A", "A6792T", "A6793G", + "A6797G", "G6798A", + "A6799G", + "G6800A", + "A6801G", "C6802A", "G6804A", "T6805A", + "C6806T", "G6811A", - "A6816-", + "A6816C", + "T6818C", "C6820A", "A6821G", "C6823T", "T6825C", - "G6826A", "A6827G", "C6828A", "T6830A", - "A6832G", "G6835A", "A6837C", "C6846A", - "A6848G", - "A6849C", - "A6851G", - "C6852T", - "G6856C", + "A6849T", "G6859A", - "A6862G", "T6864-", - "G6870T", + "G6870C", "G6872A", + "C6874A", + "C6875G", + "A6878C", "A6879C", - "A6880G", + "A6880-", + "A6882G", "T6883C", + "C6884T", "T6885C", "G6886C", "G6890C", "A6895C", + "A6897G", "A6898C", "G6899A", + "A6900C", "T6902A", + "A6903-", "C6904G", "A6906G", - "A6910C", + "G6908A", + "A6910-", + "A6911G", "A6912C", "A6913-", "G6914A", - "G6916A", + "G6916-", "T6917-", - "G6918-", + "G6918C", "G6919C", "G6921-", "G6922-", "C6924A", - "A6926G", "T6931A", "A6934G", + "C6935A", "T6940C", - "C6942A", + "A6941C", + "A6943C", "C6945T", - "A6947G", + "A6947C", "C6950A", - "T6965-", - "T6976C", + "A6968-", "C6977T", "G6981A", - "C6987A", - "C6992-", - "G6994-", - "C6999-", - "C7002-", + "A6982G", + "C6992T", + "G6994A", + "A6995G", + "C6999T", + "A7000G", + "C7002A", "A7004-", - "G7006-", - "G7007-", - "G7009-", - "G7012-", - "C7021T", + "G7006C", + "G7007A", + "A7010-", + "G7012A", + "C7013T", "T7024C", "C7028A", "A7030-", - "T7033-", - "C7034-", - "C7037T", "G7043A", "A7047C", "C7048A", - "C7054T", - "T7059C", + "C7053T", + "A7057G", + "T7059G", "C7064T", - "C7067A", - "C7068G", + "C7067-", + "C7068T", + "A7071T", "C7078T", "T7079A", - "G7080A", - "A7082G", + "G7080T", "A7084G", - "A7085T", + "A7087G", "A7089T", "C7090T", "C7094T", - "A7099G", - "C7103-", + "C7095T", + "C7103T", "A7106C", "T7109C", "C7111T", "C7117T", "C7118T", "C7120T", - "C7121T", "C7122T", - "A7125G", + "C7123-", "A7129T", - "T7135G", + "A7132G", + "C7134A", "G7136A", + "C7144-", + "A7145-", + "A7146G", + "C7147-", "C7149T", + "C7150T", + "A7155G", + "T7175A", + "C7176T", "C7178T", - "A7180G", - "T7205C", + "A7179T", "C7211T", + "A7214G", "T7217C", - "T7220C", "G7229A", - "T7232A", "C7235T", "G7244A", - "T7247C", - "T7259A", + "T7259C", "C7268T", - "A7271G", "T7280C", "C7283T", "C7284T", - "C7295T", - "A7314G", + "A7304T", + "T7322C", + "A7329G", "C7331T", "G7334A", "C7346T", - "A7348G", + "T7362A", "T7364C", "G7367A", - "A7373G", "C7385T", + "G7388A", "A7389G", "A7391G", "A7394T", "G7397A", - "C7406T", - "A7412G", + "A7403T", + "A7405-", "T7421A", - "G7427A", - "G7431A", - "A7457G", + "C7448T", "G7463A", - "G7475A", "T7484C", - "A7491C", - "C7496A", - "G7523A", - "G7532A", - "A7536-", - "A7538C", - "G7545A", - "T7547C", - "C7550A", + "A7491T", + "C7521T", + "T7535C", + "A7538T", "C7556T", "A7559C", - "A7577G", - "G7588T", + "G7561A", + "T7586C", "C7589T", + "A7595G", "T7613C", "C7619T", "C7628T", @@ -1273,344 +1320,352 @@ "G7634A", "C7638T", "G7640A", - "C7646T", "G7649A", "A7651G", - "A7655G", - "G7682A", "T7685C", - "G7688A", "T7692C", - "G7694A", "T7697C", - "A7700G", "G7710A", - "A7727G", - "A7731G", - "C7766T", + "A7721T", + "C7751T", "C7775T", "T7778C", - "C7844T", "G7849A", - "G7857A", + "T7850C", + "G7871A", "G7877A", - "G7880T", + "T7878C", "C7898T", "A7901G", - "T7907C", "G7913A", - "C7914T", - "T7934C", "T7940A", - "T7949C", "T7961A", - "C7988T", + "T7970G", + "G8011A", + "G8012A", + "A8021G", "A8048G", "A8066G", - "A8087G", + "A8082T", + "A8095C", + "C8106T", "T8107C", + "A8116T", + "T8120C", + "C8123T", "G8126A", - "T8135C", - "A8147G", + "T8127C", + "A8147C", "C8153T", + "T8159-", "G8168A", "A8177G", - "T8190A", + "G8188A", "T8195A", - "A8198G", "C8207T", "T8210C", - "A8213G", "C8216T", "T8231A", + "C8240T", + "T8249C", "A8255T", "C8258T", "T8261A", + "A8279G", "A8282G", + "T8285A", "C8318T", "C8327T", "T8330C", - "G8332A", "G8333A", "G8335T", - "G8336A", - "G8345A", - "C8366T", - "G8375A", - "C8381A", - "A8423G", - "C8426T", - "T8438C", + "A8351G", + "G8360A", + "C8381-", + "C8399T", + "C8414T", "T8441C", "G8444A", - "A8451G", "C8459T", - "A8468T", - "C8480-", - "T8493C", + "A8468C", + "C8480T", + "T8483C", "C8498T", "A8500T", - "T8511C", + "A8501G", + "T8507C", "A8526G", "G8531A", "G8543A", - "C8552T", + "C8567T", "T8588C", "T8594A", - "T8606A", - "A8612G", - "G8627A", + "T8606C", + "G8611A", + "T8613-", "A8636G", "C8642T", - "T8643C", + "G8651A", "A8653C", - "A8654G", - "C8670T", - "A8679G", - "T8701A", - "C8702A", + "A8654C", + "G8665A", + "T8696C", "A8704G", - "A8717C", + "A8711G", "C8718T", - "A8725T", "T8729C", - "G8732A", - "A8739T", "A8740G", + "C8747T", "C8750T", + "A8766C", "T8774A", + "A8786G", "T8790C", "T8798C", + "T8804C", "T8807C", - "G8816A", "C8817T", "A8825G", - "A8852G", "T8861A", "G8879A", - "C8880A", "A8891G", "G8897A", - "A8903G", "T8907C", "G8909T", "C8945T", - "T8972C", - "G8975A", "A8981T", - "C8990G", "G8996A", "T9008C", "G9022A", "A9023G", - "T9029C", - "T9038C", - "C9044T", - "T9072C", + "T9035C", + "T9071C", + "T9077C", "C9086T", "G9098A", "G9113T", "G9122A", "A9137G", "C9138T", - "A9146G", "C9156T", "C9179T", "C9182T", "A9191T", "C9206A", + "A9239G", "T9245C", - "T9251C", + "G9254A", + "T9272A", + "T9278C", "T9293C", "T9296G", - "A9305G", - "A9314G", "A9317G", + "C9318T", "C9320A", "T9335A", - "T9341C", "C9342T", "A9347G", "T9353A", "A9365G", - "A9377G", - "T9398-", - "C9404T", - "T9431A", + "A9368T", + "A9371G", + "A9383C", + "A9419C", + "T9431-", "G9443A", + "T9447A", + "G9458A", "G9476A", "T9479A", "G9480A", "T9489C", "A9491T", + "A9509C", "C9512T", + "G9514A", "T9518C", "A9521T", - "G9542T", + "G9542A", + "A9560G", "G9569A", - "C9629A", - "T9630C", + "A9596G", + "A9599G", "G9638A", - "A9644C", + "A9641T", "C9653T", + "T9660C", "G9707A", + "T9711C", "T9719C", "G9722A", + "G9725A", "C9731T", - "T9743C", "T9761C", + "T9770-", "T9773C", - "C9800T", - "C9804T", - "A9809C", + "A9788G", + "G9794A", + "A9797G", + "C9803G", + "A9809T", + "G9812A", "G9818A", "C9824T", - "A9827G", "A9833G", "T9836C", - "A9869G", - "A9870C", - "A9872G", - "G9878A", - "A9890G", + "A9851T", + "A9870T", + "A9872T", + "A9887T", "T9896C", + "C9908T", "A9929G", "C9947T", + "T9950C", "C9959T", - "T9962C", - "C9971T", - "T9980C", - "A9989G", + "T9974C", "T9998C", + "A10008T", + "T10010-", "G10018A", - "A10020G", "A10022G", "G10026A", - "C10027A", - "C10028T", "C10031T", "G10036A", + "A10043G", "G10044A", - "A10049G", + "G10046T", + "A10053C", + "T10055A", "C10071T", "G10073A", + "A10085G", "C10101T", - "G10103A", "T10121C", "A10127G", - "T10133A", + "T10130A", "C10136A", "G10142A", - "A10154G", + "A10151G", "C10169A", + "C10193A", "T10194C", - "A10214G", + "T10217C", "A10221T", "C10223T", + "C10241T", "T10244C", "G10259A", "C10262A", "T10274A", - "T10313G", - "T10314C", - "T10326C", - "T10337C", - "G10355A", - "A10370C", + "A10304G", + "A10349G", + "G10355C", "G10373A", + "A10376G", "C10379T", "C10385T", - "T10436-", + "T10389C", + "T10412C", + "C10430T", + "A10439G", "C10442T", "C10449T", - "A10463G", - "G10488A", + "C10458T", + "T10490A", + "G10491A", + "T10508A", + "C10513T", + "A10517G", + "T10520C", "G10529A", - "C10530T", + "C10530-", "G10544A", "A10547C", - "G10552A", "A10553G", - "C10557T", + "A10559G", "G10562A", - "C10567A", - "A10598G", + "G10565A", + "T10592A", + "A10601G", "C10604T", "A10614G", + "T10616A", + "C10622T", "A10632G", "C10646T", - "G10655A", "C10667T", - "G10676A", + "C10682T", + "G10690A", "A10691G", - "T10694C", + "A10706G", "A10709G", - "T10712A", "G10718A", "G10733A", "G10736A", - "A10802G", + "G10798A", + "G10805A", "A10808G", - "T10817A", + "A10829G", "A10835G", - "A10847T", - "T10853G", + "G10844A", + "T10853C", "T10854C", - "C10860A", - "T10871C", - "T10880C", - "T10883-", + "A10865G", + "C10881-", + "A10886G", "C10895T", - "T10901C", - "C10904T", - "G10931A", + "A10907G", + "T10928A", + "T10934C", + "T10946C", "C10950T", "C10955T", "C10967T", - "T11009C", + "T10979C", "T11042A", "A11066G", - "T11075C", + "T11069C", "T11081C", - "T11087C", - "T11088C", - "G11090-", + "G11090A", + "C11093G", "T11114C", - "C11123T", - "A11135T", - "A11144G", "G11156A", "T11159C", + "G11168A", "T11174C", "A11180C", "T11183C", "C11201T", - "A11210T", + "A11216T", + "G11219A", "G11228A", "G11243A", "A11249T", - "A11285T", - "T11297C", + "T11273C", + "A11285G", "G11300A", "G11309A", + "A11315G", "C11321T", "C11327T", - "T11330C", - "G11342A", + "A11348T", "C11358T", "G11360A", + "C11363T", + "T11375C", "G11387A", + "C11394T", "T11396A", + "G11402A", "G11408A", "G11417A", + "T11418C", + "A11420T", "T11426C", "T11429C", "G11450A", - "A11453G", - "T11456C", - "T11471C", - "C11474T", - "C11483T", + "T11465C", "C11492T", "G11504A", "T11513C", @@ -1618,410 +1673,415 @@ "C11543A", "T11552C", "G11573A", - "A11585G", + "C11588T", "A11589G", - "G11607A", + "T11591A", "A11618C", - "A11621T", + "A11621C", "C11628T", - "G11630A", "G11636A", "T11642C", - "T11645C", "G11669A", "T11672C", - "T11682C", - "T11690C", + "G11693A", "G11699A", "T11723C", - "T11730-", - "G11747A", "G11753A", + "T11756C", + "A11768G", "G11774A", - "T11778C", + "T11778G", + "C11779T", "C11782T", - "T11783A", "G11786A", - "G11795A", + "C11790T", + "C11816T", "T11822A", + "T11825G", + "C11826T", "G11828A", - "G11834A", - "G11840A", + "C11837T", "T11846C", - "C11852T", + "A11861G", "G11864A", "G11870A", "T11877C", - "T11881C", "A11885G", "T11912C", + "C11927T", "A11931C", "C11939T", "A11942G", "G11948A", - "A11969C", + "A11972T", + "C11974A", "G11978A", - "T11980A", "C11982T", "C11987A", - "G11994T", - "A11998G", - "T11999C", + "T12000C", "T12020C", "G12024A", - "A12025C", + "T12030C", "C12034A", "T12035C", - "C12041T", "C12052T", "C12063T", - "A12070G", - "A12087G", - "T12092C", + "C12077T", + "T12080C", + "C12094A", "T12095C", "A12101G", "C12105T", - "T12124C", - "G12128A", "G12131A", - "T12143C", "T12149C", "C12158T", - "G12186A", + "T12176A", "T12188C", + "C12192T", "A12194G", - "A12197G", + "T12206C", "A12209G", - "C12213T", + "G12218A", "T12224C", - "C12230T", + "C12225T", + "C12240T", "G12242T", "G12260A", - "C12302T", + "A12266T", + "T12269C", + "C12278-", "C12305A", "C12317T", - "T12350C", - "T12353A", + "A12320G", + "A12329G", + "T12344C", + "T12353G", "G12356A", - "C12362T", "G12365A", "A12368G", "T12371A", - "A12380T", - "G12389A", + "A12377T", + "T12381C", + "G12385A", "A12390G", "C12401T", "G12410A", "T12413A", + "A12425C", "T12455C", - "T12512C", + "A12488G", + "A12497G", + "G12515A", + "G12516A", "T12530C", "G12554A", - "C12572T", - "T12578C", + "C12581T", "T12584A", "A12585G", + "G12593A", "C12599T", - "C12602T", - "T12605C", - "C12611T", - "T12626A", + "T12626G", + "A12628T", "G12639A", + "T12650A", "G12659A", - "A12665G", + "A12665T", "A12668T", "C12671T", - "C12674T", + "T12689A", + "T12692C", + "C12696T", "C12713T", - "C12722T", "C12737T", "C12743T", - "T12747C", - "C12755T", + "C12752T", "T12776C", "G12779A", "A12784G", - "T12807C", + "T12806C", + "T12812C", "G12813T", - "T12824G", + "A12817-", + "A12818G", + "T12824C", "T12836A", - "C12845A", + "C12845T", + "T12861C", "C12870T", "G12881T", "T12887C", + "G12890A", "A12893G", + "A12900G", + "G12908A", "G12910A", "A12911G", "G12914A", + "A12917G", + "C12935T", "G12945A", "A12959C", - "T12962C", - "C12965T", "G12969A", "C12971T", - "G12977A", + "A12992G", "C12995T", - "G12998A", "A13003G", "C13004T", + "T13013C", "A13034G", - "T13058C", + "T13067C", "A13082G", "T13085C", - "T13088A", + "T13094C", "T13103C", - "A13106G", "A13109T", "T13118C", - "A13121G", - "A13136-", - "A13160G", - "G13174A", - "A13178G", - "A13181G", + "G13124A", + "A13154C", + "A13172G", "G13183A", - "A13185T", "G13190A", - "A13195C", - "A13202T", - "A13205T", - "T13206-", - "A13207-", + "A13195T", + "A13202C", + "A13205C", "G13208-", - "G13209-", - "G13211-", - "T13217C", + "G13209A", + "A13212T", + "C13213-", + "T13221C", "T13224A", - 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"I952V", "A954N", "R957K", "A960T", - "S963R", - "V1108*", "D1110N", - "R1129K", + "T1116V", + "T1134N", "T1150V", - "I1156V", "R1175K", + "R1211K", "L1239I", - "I1431V", + "M1378I", + "K1437R", "I1475V", + "V1481I", "A1539V", - "D1553E", - "F1572S", - "I1605S", + "L1602F", "P1606S", - "V1610F", "E1620T", "A1623D", - "N1635S", + "T1629A", "N1641D", - "A1643S", - "I1653T", + "A1643N", + "V1674I", "M1684I", "S1740N", "V1768I", - "D1784N", + "T1807A", + "K1821V", "V1825I", "K1873R", "A1883S", - "R1915K", - "R1916K", "V1927I", "V1935I", "T1942K", @@ -2029,120 +2089,132 @@ ], "M": [ "I23V", - "E111D" + "E111D", + "T156I", + "T241S" ], "M2-1": [ "I37L", + "R52K", + "V108I", "V130I", - "R149K", "E170D" ], "M2-2": [ "E18K", "V22K", - "D37E" + "V28A", + "D37E", + "A41N", + "N55S" ], "N": [ "A54T", "A57T", - "R96K", + "S71C", "I103V", "N106S", "D110E", - "M201F", + "M201V", "H220Y", "K356R", "V385M", - "S389N" + "S389N", + "N391D" ], "P": [ + "L19I", "R28K", "P30S", + "S35T", "I39V", "V46I", "R57K", - "T62S", + "K60R", + "P61K", "P64L", - "K74N", + "S65L", + "K74S", "G75S", "T78I", "E81T", - "I82E", - "A85T", - "I86T", - "V88T", - "P118S", + "V88P", + "M89T", + "I92V", + "L116S", + "P118F", "T122V", "P130S", "V214I", + "D221E", "S239N", "D279E", "T280I", "S284N", - "E286G", - "D287E" + "E286G" ], "SH": [ + "I2K", + "K8R", "K14E", + "T17N", "H18Q", - "K21N", - "I22T", + "D25K", "V33A", "L44F", - "T66N", "S73T", "S74P", "V80T", "T82I", + "K83R", "T84P", + "L86P", "N87D", - "D89N", + "H88L", "I90V", + "F94L", "S96R", "Y101H", - "N103D", "A105V", - "S108K", - "K113R", - "N115H", + "S108D", + "N115S", + "R116K", "T123K", "T124I", - "E133M", - "D134N", + "K131G", + "S132P", "T135S", - "N138T", + "K136T", + "T137I", "N139D", - "K142E", - "D145A", + "D141E", "R148D", "P151S", - "P153T", + "P153S", "G156E", "V157A", "H159R", - "I160T", + "I160K", "V161A", "V169I", "K170E", - "H175-", "P177L", - "T178*", - "D179E", - "E180I", + "T178I", + "D179-", + "E180K", "Q182R", - "S183L", - 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S73P, S78P, I80T, P81S, N84D, S91P, H93Q, S94A, Q97W, S101N, P106A, A108T, P112H, S113L, P117T, N125A, L127Q, V130T, S133H, P137L, R141N, T142E, V148T, H149T, K150E, I153T, T156A, T160K, P163T, P164T, A166T, K169S, A170T, V171A, P172A, R173T, V177N, R178T, S180N, S181Q, G183R, Q192R, D194R, G206T, S207R, N209T, M217T, -220T, -221E, -222K, -223H, S229T, *232S, N233L; L: D4F, N65M, S66T, V89I, D127N, E231K, D303E, T306S, N310A, Y317L, R341K, D373E, R389K, I454V, R482K, T505A, L512Q, Y520F, V537I, L761I, R783K, S896V, I948L, I949L, S963R, S1019C, V1108I, V1109I, V1116I, R1129K, N1134K, I1156V, S1538V, D1553E, F1572S, T1603N, I1605S, V1610F, A1629I, N1635S, I1653T, E1738D, I1742V, D1784N, R1915K, R1916K; M: E103D, K237R; M2-1: S88G, R149K, A169T; M2-2: N41T; N: R96K, V103G, A136V, D212E; P: K61S, T62S, I63T, T72A, I78T, I82E, I86T, P88T, S97F, T98N, I280T, D287E; SH: R8K, I50V, I61A, T66N, P74K, S75L, T85I, D89N, T91V, S104F, N107K, K113R, S115H, P132F, E133I, D134N, I137G, N138T, K142E, D145A, N149K, S153T, A154M, A157K, Y158H, I166L, Y167H, I169T, K172G, H175-, I178*, *184S", "clade": "B" } }, @@ -3348,7 +3349,7 @@ { "name": "NODE_0000002", "node_attrs": { - "div": 0.103, + "div": 0.102, "clade_membership": { "value": "B1" } @@ -3357,44 +3358,50 @@ "mutations": { "nuc": [ "A186G", + "G189A", "T207C", "A228T", - "A288G", + "G255A", "T348C", "A438G", "G492A", "T538C", + "C577T", "C603T", "T696C", + "C801T", "A811C", "T843C", "G877T", "A888G", - "C894T", "A972G", - "G1065A", "A1143G", - "C1152T", "A1199G", "A1268G", "A1307C", "A1346G", "A1442G", + "G1445A", "C1477T", "C1486T", "A1498C", + "A1500G", "G1550A", + "C1555T", "A1598G", "C1600T", "A1609G", + "T1658C", "A1736G", "G1741A", "A1781T", "A1796G", + "A1857C", + "A1910G", "A1916T", "C1940T", "G1955A", - "G1970A", + "A1958G", "T2021C", "C2117T", "C2203A", @@ -3402,22 +3409,22 @@ "T2227C", "C2242T", "A2248G", + "G2302A", "C2311T", "A2389T", "A2431G", - "T2483C", "A2485G", "C2521T", "A2530G", + "T2533C", "G2602A", + "A2731G", "A2743G", "A2749G", "A2842G", - "C2860T", - "T2937C", - "C2946T", - "T2965C", + "C2966T", "-3006A", + "C3016T", "A3022G", "A3105G", "A3111G", @@ -3431,126 +3438,129 @@ "C3283T", "A3288G", "T3303C", + "A3330G", + "G3357A", "C3390T", "A3478C", "C3483T", - "C3730T", "T3795C", - "G3804A", - "C3864T", "G3867A", "C3868T", "A3942G", "C4161A", - "A4197G", "C4206T", - "-4215A", "C4258T", "C4293T", "T4320C", "G4344A", - "A4455G", - "G4617A", - "T4641C", + "A4543G", "A4790G", "G4796T", "C4808T", "A5006C", - "T5033C", "T5059C", "T5081C", "C5096T", - "A5111G", - "T5114C", + "C5162T", "A5192G", "A5215G", - "T5253C", "G5301A", + "A5349T", "C5409T", "T5418C", "A5538G", "T5558C", - "A5574G", - "C5610T", + "T5614C", + "T5684C", "A5708T", "C5724T", "T5748A", "A5759C", "G5769T", + "A5792G", "A5817T", "C5823T", "C5850T", - "T5889C", "A5902G", "A5903G", + "A5916G", "T5928C", "C5945T", - "T6012C", - "-6025A", "G6028-", + "A6029-", "A6032-", + "T6036A", "T6070C", + "A6088G", "A6090G", + "T6111-", + "C6112-", "A6127G", "T6130G", - "G6145A", + "A6158G", "T6177C", "A6276G", "G6300A", "A6323G", + "T6358C", "A6366G", "T6372C", "T6390C", "T6403C", "C6425T", - "G6432A", - "C6436A", "C6454T", - "T6458C", "T6489C", - "G6490A", - "T6494C", "A6497G", + "T6499C", "G6525A", - "-6536G", + "T6536G", "C6586T", "C6602A", + "T6612C", "A6649G", "G6659A", "C6677T", "C6689A", - "A6694C", + "G6694C", "A6699C", "C6713A", "C6716A", + "A6718G", "C6719G", + "C6720A", + "A6724G", + "G6727A", "A6729C", + "C6732A", "C6734A", "C6737A", + "C6739A", "C6746G", "A6751G", + "C6753T", "G6757A", + "C6762A", "C6789A", "G6794C", "A6798T", - "C6806T", "C6818A", "T6823C", "A6830C", "G6833A", "A6858G", "A6899G", - "A6911G", + "A6908G", "-6917C", "-6922A", "G6934C", - "-6965C", + "-6968A", + "T6976C", "A6979G", "T6983-", "T6990-", "G6991-", "A6993-", - "A6995-", + "A6994-", "C6996-", "T7005-", "T7031-", @@ -3561,26 +3571,24 @@ "T7062G", "T7075A", "T7078A", - "A7080T", "A7108G", "C7158T", "A7163G", + "A7175C", "C7187T", + "T7205C", "T7250C", + "C7259A", "A7343G", - "C7448T", "A7472G", - "C7538T", "T7580C", "T7607C", - "G7655A", - "G7727A", "A7772C", - "T7878C", "T7886C", + "T7934C", "T7943C", + "T7949C", "A7967T", - "A7970G", "C7988A", "T8009A", "A8060G", @@ -3588,24 +3596,24 @@ "C8120A", "T8138C", "G8139A", + "C8147T", "T8183C", "T8192C", + "A8198G", + "G8336A", "C8342T", + "C8468T", "A8528G", "A8537G", "T8546C", "C8552A", - "T8613C", "T8639C", "A8645G", - "A8816G", "A8828G", "T8910C", - "G8990A", "T9005C", "T9032C", "C9059T", - "C9072T", "A9089G", "C9116A", "A9131T", @@ -3618,70 +3626,67 @@ "A9484G", "C9509T", "C9524T", - "A9560G", + "G9596A", "C9644T", "C9668T", + "A9725G", "A9728G", "A9776G", "C9783T", - "T9800C", - "G9869A", - "T9974C", "A10038G", "C10238T", "C10244T", "A10253G", "A10262T", "T10292C", - "A10304G", "C10388T", "T10550C", "A10757G", "C10772T", "T10838C", + "T11009C", "T11175C", "C11183T", "T11264C", + "T11330C", "C11381T", + "C11483T", "A11501C", "A11529G", "C11576T", "G11582A", + "A11585G", "T11648C", "G11687A", "A11717G", + "G11768A", "A11780G", - "A11795G", - "C11826T", "T11856C", "T11897A", "G11945A", - "G11998A", "A12008G", "A12046G", "A12059G", "T12155C", "A12179T", "C12224T", - "T12381C", + "C12230T", + "C12302T", "A12392G", "T12545C", "A12569C", "A12627G", - "C12628T", "G12698A", - "C12807T", - "A12818G", + "A12824G", "A12872G", "C12932T", + "T12935C", "C13118T", "G13133A", "A13139G", "A13151G", - "-13206C", - "-13207A", + "C13202T", "-13208T", - "A13252G", "-13300C", "T13314-", "A13326C" @@ -3690,27 +3695,26 @@ "I498V" ], "G": [ - "M18I", "K26R", "Y53H", "T60I", "H64N", + "P70S", "D84G", - "D101N", - "H114Y", "P119Q", - "A123T", "S126P", "T135A", - "S138K", + "R138K", "T144I", "K159Q", "T163K", "T164G", "R165K", - "R166E", + "T166E", "T189I", + "A191D", "S193P", + "N195T", "S196D", "S215-", "T230Q", @@ -3722,10 +3726,8 @@ "K773R", "H873Y", "N958D", - "V1431I", "I1455V", - "K1627R", - "T1821V" + "K1627R" ], "M2-1": [ "E20D", @@ -3738,26 +3740,25 @@ "D387G" ], "P": [ + "S74N", "A77V", "T80I", "Q84P", - "T85A", - "S118F", "N121S", "R165K" ], "SH": [ + "I22T", "D72V", "N89T", "Q92H", - "M133I", - "N137G", + "D108S", "S151L", - "E179-" + "K180I" ] }, "labels": { - "aa": "F: I498V; G: M18I, K26R, Y53H, T60I, H64N, D84G, D101N, H114Y, P119Q, A123T, S126P, T135A, S138K, T144I, K159Q, T163K, T164G, R165K, R166E, T189I, S193P, S196D, S215-, T230Q, S234P; L: D325N, E698Q, K773R, H873Y, N958D, V1431I, I1455V, K1627R, T1821V; M2-1: E20D, I108T, K160R; N: M258L, A280S, D387G; P: A77V, T80I, Q84P, T85A, S118F, N121S, R165K; SH: D72V, N89T, Q92H, M133I, N137G, S151L, E179-", + "aa": "F: I498V; G: K26R, Y53H, T60I, H64N, P70S, D84G, P119Q, S126P, T135A, R138K, T144I, K159Q, T163K, T164G, R165K, T166E, T189I, A191D, S193P, N195T, S196D, S215-, T230Q, S234P; L: D325N, E698Q, K773R, H873Y, N958D, I1455V, K1627R; M2-1: E20D, I108T, K160R; N: M258L, A280S, D387G; P: S74N, A77V, T80I, Q84P, N121S, R165K; SH: I22T, D72V, N89T, Q92H, D108S, S151L, K180I", "clade": "B1" } }, @@ -3765,7 +3766,7 @@ { "name": "NODE_0000003", "node_attrs": { - "div": 0.113, + "div": 0.112, "clade_membership": { "value": "B1" } @@ -3816,6 +3817,7 @@ "G4604A", "C4613A", "C4650A", + "G4748A", "A4802G", "T4889C", "T4964C", @@ -3826,7 +3828,6 @@ "G5935A", "C5952T", "A5960G", - "G6114A", "A6132G", "T6159C", "G6165A", @@ -3847,6 +3848,7 @@ "C6599T", "C6643T", "A6701G", + "G6712A", "A6720G", "C6747T", "G6797A", @@ -3867,10 +3869,9 @@ "-6997A", "-6998C", "-6999C", - "-7002A", "-7004A", "A7008-", - "-7012C", + "A7012C", "C7014A", "A7018T", "T7021A", @@ -3887,7 +3888,6 @@ "A8846G", "C9008T", "T9804C", - "G9812A", "A9848T", "C9897A", "A9938G", @@ -3905,12 +3905,11 @@ "T11787C", "T12005A", "A12365G", - "C12752T", "C12806T", "G12896A", "A12945G", "A13010T", - "-13279A" + "-13278T" ], "F": [ "K479R", @@ -3973,14 +3972,14 @@ "author": "Piyaratna,R.,Tollefson,S.J.,Williams,J.V.,Piyaratna,R.V.", "value": "Piyaratna,R.,Tollefson,S.J.,Williams,J.V.,Piyaratna,R.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B1" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -4084,14 +4083,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B1" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -4148,14 +4147,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B1" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -4187,14 +4186,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B1" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -4239,7 +4238,6 @@ "A3587G", "C4317T", "T4443C", - "A4748G", "G4865A", "T4886A", "G5449A", @@ -4249,13 +4247,13 @@ "-6026A", "-6109C", "T6113-", + "A6114G", "A6416G", "T6560C", "T6571C", "T6584C", "G6657A", "C6669T", - "A6712G", "T6741C", "C6785T", "C6831T", @@ -4280,10 +4278,10 @@ "-6986A", "A7000-", "A7001-", + "A7002-", "A7003-", "-7009A", "-7010A", - "-7012A", "G7019T", "T7020A", "T7024A", @@ -4305,12 +4303,14 @@ "T8699C", "C8895T", "C9245T", + "A9812G", "T9824C", "C10058T", "A10616G", "T10871C", "C12411T", "C12569T", + "T12752C", "C13119T" ], "F": [ @@ -4341,7 +4341,7 @@ { "name": "PP862723", "node_attrs": { - "div": 0.123, + "div": 0.122, "clade_membership": { "value": "B1" } @@ -4585,7 +4585,7 @@ { "name": "NODE_0000007", "node_attrs": { - "div": 0.117, + "div": 0.116, "clade_membership": { "value": "B1" } @@ -4698,7 +4698,7 @@ "T13275-", "T13276-", "A13277-", - "T13278-", + "A13279-", "A13280-", "A13281-", "-13283T", @@ -4742,7 +4742,7 @@ { "name": "NODE_0000008", "node_attrs": { - "div": 0.126, + "div": 0.125, "clade_membership": { "value": "B1" } @@ -4907,20 +4907,20 @@ { "name": "KJ627435", "node_attrs": { - "div": 0.127, + "div": 0.126, "accession": "KJ627435", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "B1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -4967,14 +4967,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "B1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -5002,7 +5002,7 @@ { "name": "NODE_0000009", "node_attrs": { - "div": 0.117, + "div": 0.116, "clade_membership": { "value": "B1" } @@ -5031,14 +5031,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -5232,7 +5232,7 @@ { "name": "NODE_0000010", "node_attrs": { - "div": 0.12, + "div": 0.119, "clade_membership": { "value": "B1" } @@ -5287,7 +5287,7 @@ { "name": "NODE_0000011", "node_attrs": { - "div": 0.122, + "div": 0.121, "clade_membership": { "value": "B1" } @@ -5370,14 +5370,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": 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"value": "B1" } @@ -6455,14 +6455,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "B1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -6525,20 +6525,20 @@ { "name": "KJ627383", "node_attrs": { - "div": 0.135, + "div": 0.134, "accession": "KJ627383", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "B1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -6625,7 +6625,7 @@ { "name": "NODE_0000018", "node_attrs": { - "div": 0.125, + "div": 0.124, "clade_membership": { "value": "B1" } @@ -6692,7 +6692,7 @@ { "name": "NODE_0000019", "node_attrs": { - "div": 0.125, + "div": 0.124, "clade_membership": { "value": "B1" } @@ -6709,20 +6709,20 @@ { "name": "KF530171", "node_attrs": { - "div": 0.125, + "div": 0.124, "accession": "KF530171", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -6736,20 +6736,20 @@ { "name": "KF530164", "node_attrs": { - "div": 0.125, + "div": 0.124, "accession": "KF530164", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -6775,7 +6775,7 @@ { "name": "NODE_0000020", "node_attrs": { - "div": 0.125, + "div": 0.124, "clade_membership": { "value": "B1" } @@ -6793,20 +6793,20 @@ { "name": "KF530167", "node_attrs": { - "div": 0.126, + "div": 0.125, "accession": "KF530167", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -6852,7 +6852,7 @@ { "name": "NODE_0000021", "node_attrs": { - "div": 0.125, + "div": 0.124, "clade_membership": { "value": "B1" } @@ -6871,6 +6871,34 @@ } }, "children": [ + { + "name": "KF530173", + "node_attrs": { + "div": 0.124, + "accession": "KF530173", + "author": { + "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", + "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." + }, + "clade_membership": { + "value": "B1" + }, + "region": { + "value": "Oceania" + }, + "country": { + "value": "Australia" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C5700T", + "A12854G" + ] + } + } + }, { "name": "KF530177", "node_attrs": { @@ -6880,14 +6908,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -6918,34 +6946,6 @@ "aa": "L: K349-, N350-, P1339S, A1550G, A1586-" } } - }, - { - "name": "KF530173", - "node_attrs": { - "div": 0.125, - "accession": "KF530173", - "author": { - "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", - "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." - }, - "country": { - "value": "Australia" - }, - "region": { - "value": "Oceania" - }, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C5700T", - "A12854G" - ] - } - } } ] } @@ -6960,7 +6960,7 @@ { "name": "NODE_0000022", "node_attrs": { - "div": 0.123, + "div": 0.122, "clade_membership": { "value": "B1" } @@ -6990,6 +6990,7 @@ "C6865T", "A6941C", "T6944A", + "C6945T", "G7059A", "T7325C", "A7865G", @@ -7056,7 +7057,7 @@ { "name": "NODE_0000024", "node_attrs": { - "div": 0.124, + "div": 0.123, "clade_membership": { "value": "B1" } @@ -7074,20 +7075,20 @@ { "name": "KF530179", "node_attrs": { - "div": 0.125, + "div": 0.124, "accession": "KF530179", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -7109,7 +7110,6 @@ "G6712A", "G6938C", "G6939A", - "C6945T", "-6984A", "-6989A", "G7110A", @@ -7149,20 +7149,20 @@ { "name": "KF530182", "node_attrs": { - "div": 0.125, + "div": 0.124, "accession": "KF530182", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -7278,20 +7278,20 @@ { "name": "KF530181", "node_attrs": { - "div": 0.13, + "div": 0.129, "accession": "KF530181", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -7384,20 +7384,20 @@ { "name": "KF530158", "node_attrs": { - "div": 0.129, + "div": 0.128, "accession": "KF530158", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -7512,6 +7512,8 @@ "A6980-", "A6985-", "A6986-", + "C6987-", + "C6988-", "A7012-", "G7029A", "T8744C", @@ -7580,14 +7582,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -7703,14 +7705,14 @@ "author": "Lu,L.,Robertson,G.,Ashworth,J.,Pham Hong,A.,Shi,T.,Ivens,A.,Thwaites,G.,Baker,S.,Woolhouse,M.", "value": "Lu,L.,Robertson,G.,Ashworth,J.,Pham Hong,A.,Shi,T.,Ivens,A.,Thwaites,G.,Baker,S.,Woolhouse,M." }, - "country": { - "value": "Vietnam" + "clade_membership": { + "value": "B1" }, "region": { "value": "Asia" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Vietnam" } }, "branch_attrs": { @@ -7819,13 +7821,10 @@ "T6923C", "G6938C", "G6939A", - "C6945T", "C6976-", "T6977-", "T6978-", "G6979-", - "C6987-", - "C6988-", "-7004A", "-7005T", "-7006T", @@ -8015,7 +8014,7 @@ { "name": "NODE_0000028", "node_attrs": { - "div": 0.131, + "div": 0.13, "clade_membership": { "value": "B1" } @@ -8048,7 +8047,6 @@ "G6908A", "A6916G", "C6941A", - "A7008-", "A7009-", "A7024T", "T7027A", @@ -8102,20 +8100,20 @@ { "name": "MH828687", "node_attrs": { - "div": 0.137, + "div": 0.136, "accession": "MH828687", "author": { "author": "Lu,L.,Robertson,G.,Ashworth,J.,Pham Hong,A.,Shi,T.,Ivens,A.,Thwaites,G.,Baker,S.,Woolhouse,M.", "value": "Lu,L.,Robertson,G.,Ashworth,J.,Pham Hong,A.,Shi,T.,Ivens,A.,Thwaites,G.,Baker,S.,Woolhouse,M." }, - "country": { - "value": "Vietnam" + "clade_membership": { + "value": "B1" }, "region": { "value": "Asia" }, - "clade_membership": { - "value": "B1" + "country": { + "value": "Vietnam" } }, "branch_attrs": { @@ -8172,8 +8170,7 @@ "T6923C", "C6934T", "A6944T", - "C6987-", - "C6988-", + "T6945C", "-6994G", "-6995A", "-6996A", @@ -8185,6 +8182,7 @@ "-7002A", "-7003A", "-7004A", + "A7008-", "A7010-", "A7011-", "G7472A", @@ -8342,12 +8340,12 @@ "C6917T", "T6942C", "C6943T", - "C6945T", "-6984A", "-6985A", "-6986A", + "-6987C", + "-6988C", "-6989A", - "-7008A", "-7009A", "-7012A", "T7026C", @@ -8469,20 +8467,12 @@ "branch_attrs": { "mutations": { "nuc": [ - "A5474-", - "T5475-", - "A6027T", + "A6028-", "T6029-", - "A6030-", "T6032-", "T6929C", - "T7014-", "A7018-", - "T7019-", "A7020-", - "T7021-", - "G7028-", - "A7029-", "A13214-", "T13218-", "C13221T", @@ -8495,23 +8485,21 @@ "A13233G" ], "SH": [ - "K178N", - "I179-", - "I180T", - "R182A", + "I179N", + "I180-", "L183F", "S184N" ] }, "labels": { - "aa": "SH: K178N, I179-, I180T, R182A, L183F, S184N" + "aa": "SH: I179N, I180-, L183F, S184N" } }, "children": [ { - "name": "NODE_0000031", + "name": "MZ504959", "node_attrs": { - "div": 0.134, + "div": 0.141, "clade_membership": { "value": "B1" } @@ -8519,401 +8507,209 @@ "branch_attrs": { "mutations": { "nuc": [ + "A18C", + "A19T", + "C20A", + "A21G", + "A22G", + "A23T", + "-24A", + "C26A", + "G27C", + "A30G", + "A36-", + "A51G", + "G372T", + "C720T", + "C993T", + "T1554C", + "T1806C", + "A1904T", + "T2933C", + "C3038T", + "C3918T", + "A3960G", + "G4455A", + "C4644T", + "A4847G", + "C5316T", + "G5956A", + "-6028T", "-6029A", - "A6036T", - "C6037-", - "G6038-", - "G6039-", - "C6040-" + "A6031T", + "-6032A", + "A6034C", + "C6035A", + "A6036C", + "C6037G", + "G6039C", + "C6040T", + "T6043C", + "C6044A", + "A6046C", + "C6047A", + "A6048T", + "T6050G", + "G6051A", + "A6053-", + "T6166-", + "C6167-", + "A6168-", 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"-7027A", + "-7028G", + "-7029A", "G8213A", "C11261A", - "A11582G", "A13044G" ], "F": [ @@ -10468,7 +9551,6 @@ "Y114H", "T118A", "Q119R", - "T134I", "E142T", "Q143T", "T144E", @@ -10498,6 +9580,7 @@ "Q181R", "I182D", "R183A", + "N184S", "A185E", "S186T", "E187I", @@ -10509,9 +9592,6 @@ "M": [ "P29S" ], - "P": [ - "T120A" - ], "SH": [ "I85M", "I106M", @@ -10532,21 +9612,21 @@ "R159G", "K160G", "I168V", - "Y177W", + "*177W", "N178D", - "-179G", + "N179G", "N184G" ] }, "labels": { - "aa": "F: Q307R; G: N7S, I11M, M13V, K15E, K17R, I18M, K19E, R23G, Y28C, R29G, T39A, N46S, I47V, I51V, K61R, K75R, T80A, N86D, K88E, T99A, N101S, T103A, F104L, Y114H, T118A, Q119R, T134I, E142T, Q143T, T144E, T145R, E146G, K147T, T149G, E150A, K151T, K152T, T153Q, T154K, K156E, E158G, T167-, T168-, S169A, T170A, A172Q, T173A, Q174A, T175N, N177T, T178N, T179Q, N180I, Q181R, I182D, R183A, A185E, S186T, E187I, I189T; L: K1960E; M: P29S; P: T120A; SH: I85M, I106M, K107E, T120A, I122V, K123E, I124V, I133V, T136A, K141G, T144A, K149R, K150R, K152E, T153A, K157R, R159G, K160G, I168V, Y177W, N178D, -179G, N184G" + "aa": "F: Q307R; G: N7S, I11M, M13V, K15E, K17R, I18M, K19E, R23G, Y28C, R29G, T39A, N46S, I47V, I51V, K61R, K75R, T80A, N86D, K88E, T99A, N101S, T103A, F104L, Y114H, T118A, Q119R, E142T, Q143T, T144E, T145R, E146G, K147T, T149G, E150A, K151T, K152T, T153Q, T154K, K156E, E158G, T167-, T168-, S169A, T170A, A172Q, T173A, Q174A, T175N, N177T, T178N, T179Q, N180I, Q181R, I182D, R183A, N184S, A185E, S186T, E187I, I189T; L: K1960E; M: P29S; SH: I85M, I106M, K107E, T120A, I122V, K123E, I124V, I133V, T136A, K141G, T144A, K149R, K150R, K152E, T153A, K157R, R159G, K160G, I168V, *177W, N178D, N179G, N184G" } } }, { - "name": "MZ504960", + "name": "OP904074", "node_attrs": { - "div": 0.141, + "div": 0.139, "clade_membership": { "value": "B1" } @@ -10554,121 +9634,100 @@ "branch_attrs": { "mutations": { "nuc": [ - "A17C", - "A18C", - "C20A", - "-24A", - "A34T", - "T35-", - "A36-", - "A1889G", - 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+ "G": [ + "P126L", + "I140T", + "E210G" + ], + "L": [ + "I115M", + "I548V", + "N1038S" + ], + "SH": [ + "G137S" + ] + }, + "labels": { + "aa": "G: P126L, I140T, E210G; L: I115M, I548V, N1038S; SH: G137S" + } + }, + "children": [ + { + "name": "OP904061", + "node_attrs": { + "div": 0.145, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C474T", + "G912A", + "T1200C", + "T1340C", + "C1343T", + "C1421T", + "T1973C", + "C1988T", + "A2081T", + "C3056T", + "C3075T", + "T3609C", + "C4185T", "A4329G", "G4749A", "G5340A", @@ -10986,7 +10819,6 @@ "-6028A", "-6029A", "-6030T", - "-6031A", "-6032A", "A6033C", "A6036G", @@ -11006,6 +10838,8 @@ "A6164G", "T6269C", "T6489C", + "T6513C", + "T6572C", "C6583T", "T6653C", "T6831C", @@ -11027,14 +10861,10 @@ "-7004A", "-7005T", "-7006T", - "C7013-", - "A7016-", - "A7022-", + "-7007T", + "-7009G", "A7040G", "-7041G", - "-7042A", - "-7043A", - "-7044A", "G7060A", "G7839A", "G8090A", @@ -11063,6 +10893,7 @@ ], "G": [ "I8T", + "L109P", "P113S", "L136P" ], @@ -11088,17 +10919,17 @@ "L176Y", "Y177P", "N178Y", - "-179N", - "-180N" + "-180N", + "R182A" ] }, "labels": { - "aa": "F: S2F; G: I8T, P113S, L136P; L: V225I, T960I, I1035V, V1351A, A1600T; M2-1: A5T; M2-2: M31I; P: K278N; SH: T120I, Y175-, L176Y, Y177P, N178Y, -179N, -180N" + "aa": "F: S2F; G: I8T, L109P, P113S, L136P; L: V225I, T960I, I1035V, V1351A, A1600T; M2-1: A5T; M2-2: M31I; P: K278N; SH: T120I, Y175-, L176Y, Y177P, N178Y, -180N, R182A" } } }, { - "name": "NODE_0000045", + "name": "NODE_0000044", "node_attrs": { "div": 0.142, "clade_membership": { @@ -11108,52 +10939,50 @@ "branch_attrs": { "mutations": { "nuc": [ - "C3712T", - "C3795T", - "A6161G", - "C6896T", - "T6944A", - "-7012C", - "-7014A", - "-7015G", - "-7017G", + "A6031-", + "G6688A", + "A6689C", + "A6691C", + "C6693G", + "C6694A", + "A6695G", + "G6696A", + "G6698A", + "C6699A", + "A6701G", + "C6702A", + "A6703C", + "C6705A", + "A7008-", + "-7015A", + "-7016A", + 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+ "name": "NODE_0000051", "node_attrs": { - "div": 0.151, + "div": 0.146, "clade_membership": { "value": "B1" } @@ -12813,104 +11709,61 @@ "branch_attrs": { "mutations": { "nuc": [ - "T714A", - "A723G", - "A1065G", - "T1352C", + "C996T", + "C1409T", "C1433T", - "A1482C", - "G1491A", - "C1497A", - "T1522C", - "T1536C", - "T1763C", - "T1826C", - "T1973C", - "G3315A", - "C3432A", - "A3798T", - "C3939T", - "G4092A", - "G4428A", - "G4605A", - "C5709T", - "G5917A", - "C6038T", - "G6459A", - "C6518T", - "C6580T", - "C6612T", - "G6899A", - "A7130G", - "G7138A", - "C7325T", - "C7544T", - "A8084G", - "C8192T", - "C8729T", - "A9177G", - "C9185T", - "A9623G", - "A9707G", - "G9725A", - "C9974T", - "T10301C", - "T11087C", - "T11187C", - "T11631C", - "C11988A", - "A12024G", - "A12557G", - "A13284G", - "A13299G" + "A1970G", + "C3135T", + "G5204A", + "A5470T", + "T5473A", + "-5474A", + "-5475T", + "C5952T", + "T6024A", + "T6027A", + "-6028A", + "-6029T", + "-6030A", + "-6031A", + "-6032T", + "C6037T", 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I180T" } } }, { - "name": "PP947634", + "name": "NODE_0000052", "node_attrs": { - "div": 0.151, + "div": 0.147, "clade_membership": { "value": "B1" } @@ -13043,63 +11845,155 @@ "branch_attrs": { "mutations": { "nuc": [ - "A81G", - "T456C", - "G693A", - "C699T", - "A978G", - "G1532A", - "T2114C", - "T2275C", - "T2306C", - "T2311C", - "T2341C", - "G3587A", - "C3939T", - "C4128T", - "C4443T", - "C4653T", - "G4970A", - "G5201A", - "G6264A", - "T6387C", - "G6423A", - "A6602G", + "T2111C", + "C2392T", + "C3159T", + "T3207A", + "T4077C", + "C5900T", + "A6342T", "C6965A", - "G7017A", - "T7187A", - "A8720G", - "A8732G", - "C8936T", - "C8963T", - "A9275G", - "T10229C", - "C10520T", - "T11087C", - "T11682C", - "C11779T", - "A11870G", - "G12098A", - "G12561A", - "C13143T" - ], - "F": [ - "R179K" - ], - "G": [ - "M59I", - "Q119R" + "C9311T", + "A9716G", + "A11462G", + "T12569C" ], - "L": [ - "S1506P", - "A1538V", - "V1799I" + "SH": [ + "T136I" ] }, "labels": { - "aa": "F: R179K; G: M59I, Q119R; L: S1506P, A1538V, V1799I" + "aa": "SH: T136I" } - } + }, + "children": [ + { + "name": "PP947667", + "node_attrs": { + "div": 0.15, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A345G", + "A473G", + "T549C", + "G662A", + "C720T", + "T1379C", + "C1703T", + "C1730T", + "A2413G", + "T2941C", + "T2942C", + "T2957C", + "A3063G", + "C3102T", + "G3327A", + "C3498T", + "A3645G", + "T3924C", + "T4116C", + "G4479A", + "T4676C", + "C4946T", + "A5364G", + "G5607A", + "C6108A", + "C6109-", + "-6112T", + "-6113C", + "T6556C", + "C7049T", + "G7343A", + "A7362G", + "A8531G", + "T9578C", + "T9866C", + "G9875A", + "A10055T", + "G10349A", + "C12446T", + "T12746C" + ], + "G": [ + "F104L" + ], + "L": [ + "T66A" + ], + "N": [ + "N145S", + "R208K" + ] + }, + "labels": { + "aa": "G: F104L; L: T66A; N: N145S, R208K" + } + } + }, + { + "name": "PP947652", + "node_attrs": { + "div": 0.15, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G12A", + "A2075G", + "T2099C", + "T2275G", + "G2377A", + "A4612G", + "T5856C", + "A6688-", + "C6689A", + "G6693C", + "A6700G", + "G6701A", + "A6702C", + "C6703A", + "A6705C", + "C6707A", + "A6708G", + "G6711C", + "G6712A", + "A6714C", + "A6717C", + "G6718C", + "G6719C", + "G6720C", + "G6724A", + "T7217C", + "A7736G", + "A7916G", + "G8666A", + "C8680T", + "C8936T" + ], + "F": [ + "T521A" + ], + "G": [ + "T148-" + ], + "L": [ + "A505V" + ] + }, + "labels": { + "aa": "F: T521A; G: T148-; L: A505V" + } + } + } + ] } ] } @@ -13108,7 +12002,7 @@ ] }, { - "name": "NODE_0000064", + "name": "NODE_0000053", "node_attrs": { "div": 0.144, "clade_membership": { @@ -13116,13 +12010,40 @@ } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "A5470T", + "T5473A", + "T6024A", + "T6513C", + "T6572C", + "C6691A", + "G6695A", + "A6702C", + "T6944A", + "-7024T", + "-7027A", + "-7028C", + "-7029A", + "-7031C", + "C7045-", + "A7046C", + "A7048C", + "C7051T" + ], + "G": [ + "L109P" + ] + }, + "labels": { + "aa": "G: L109P" + } }, "children": [ { - "name": "NODE_0000065", + "name": "NODE_0000054", "node_attrs": { - "div": 0.144, + "div": 0.152, "clade_membership": { "value": "B1" } @@ -13130,16 +12051,210 @@ "branch_attrs": { "mutations": { "nuc": [ - "A10733T", - "T12191C" + "T87A", + "A118C", + "G396A", + "G861A", + "G1143A", + "C1233A", + "A1345G", + "A1417G", + "G2009A", + "C2039T", + "G2659A", + "G2845A", + "G3023A", + "T3038C", + "T3138C", + "T3222C", + "C3252T", + "G3789A", + "T3969C", + "G4428A", + "T4745C", + "C5253T", + "T5445C", + "-5474A", + "-5475T", + "A5526T", + "G5790A", + "T6020C", + "T6027A", + "-6028A", + "-6029T", + "-6030A", + "-6031A", + "-6032T", + "C6189-", + "C6190-", + "A6191-", + "T6192-", + "A6193-", + "A6194-", + "T6195C", + "-6196C", + "C6202A", + "A6203C", + "C6204A", + "T6205A", + "G6206T", + "A6207C", + "G6208A", + "T6209C", + "-6210T", + "-6211G", + "-6212A", + "-6213G", + "-6214T", + "-6215A", + "A6217-", + 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"branch_attrs": { "mutations": { "nuc": [ - "G1198A", - "C6458T", - "C6494T" + "G363A", + "A5926G", + "C6886-", + "A6888T", + "-6889A", + "C10556T" ], "G": [ - "A71V", - "A83V" + "P214-" ], - "N": [ - "G387S" + "SH": [ + "T145A" ] }, "labels": { - "aa": "G: A71V, A83V; N: G387S" - } - }, - "children": [ - { - "name": "OP904082", - "node_attrs": { - "div": 0.147, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1152C", - "A2812G", - "A2848T", - "T3868C", - "A4032G", - "G4608A", - "T4940C", - "T6066A", - "A6150G", - "T6405C", - "A6417G", - "C6479T", - "G6719A", - "A6757G", - "C6844A", - "T7202C", - "G7433A", - "G7472A", - "T7628C", - "A7835C", - "C8936T", - "A9627G", - "G9929A", - "G10127A", - "C10194T", - "A11051G", - "T11975C", - "T12182C", - "T12251C", - "T12323C", - "G12392A", - "T12746C" - ], - "G": [ - "P78L", - "G160E", - "T173A", - "Q200K" - ], - "L": [ - "M89I", - "I821V" - ] - }, - "labels": { - "aa": "G: P78L, G160E, T173A, Q200K; L: M89I, I821V" - } - } - }, - { - "name": "OP904035", - "node_attrs": { - "div": 0.147, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A963G", - "C1724T", - "G2210T", - "T2272C", - "A2914G", - "G3105A", - "C3523T", - "T3924C", - "T4623C", - "C4653T", - "A5320G", - "C5369T", - "G5538A", - "G5706A", - "G6009A", - "G6534A", - "A6585T", - "C6929A", - "C7907T", - "G8099A", - "T8327C", - "T9095C", - "A9425G", - "G9484A", - "T10097C", - "A10841G", - "T10882C", - "A11453G", - "A11462G", - "G12098A", - "T12299A" - ], - "G": [ - "K147E" - ], - "L": [ - "R773K", - "I1239T" - ], - "M": [ - "A16S" - ], - "M2-2": [ - "T25A", - "T41I" - ] - }, - "labels": { - "aa": "G: K147E; L: R773K, I1239T; M: A16S; M2-2: T25A, T41I" - } - } + "aa": "G: P214-; SH: T145A" } - ] + } }, { - "name": "NODE_0000067", + "name": "NODE_0000055", "node_attrs": { - "div": 0.145, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -13300,58 +12292,39 @@ "branch_attrs": { "mutations": { "nuc": [ - "G2815A", - "G3321A", - "G4749A", - "G5538A", - "A5722G", - "G6880A", - "A8288G", - "A11822G", - "T12248C", - "G12794A" + "A5351C", + "A6346G", + "T9527C", + "G12497A" ], "G": [ - "G212S" - ], - "M2-1": [ - "A5T" + "I34V" ], - "SH": [ - "T77A" + "M2-2": [ + "H35P" ] }, "labels": { - "aa": "G: G212S; M2-1: A5T; SH: T77A" + "aa": "G: I34V; M2-2: H35P" } }, "children": [ { - "name": "NODE_0000068", + "name": "NODE_0000056", "node_attrs": { - "div": 0.145, + "div": 0.153, "clade_membership": { "value": "B1" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A3822G", - "T3951C", - "T4386C", - "C5033T", - "G7574A", - "G10709A", - "T11876C" - ] - } + "mutations": {} }, "children": [ { - "name": "PP947585", + "name": "PP947694", "node_attrs": { - "div": 0.151, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -13359,110 +12332,17 @@ "branch_attrs": { "mutations": { "nuc": [ - "A525G", - "T864C", - "G975A", - "T1101C", - "G1119A", - "A1512C", - "T1826C", - "C2228T", - "A2320G", - "A2458G", - "C2722T", - "T2729C", - "T2872C", - "A3012G", - "G3288A", - "G3315A", - "A3894G", - "G4131A", - "C4263T", - "C4817T", - "C5028T", - "C5174T", - "A5470T", - "T5473A", - "-5474A", - "-5475T", - "G5616A", - "A5694G", - "C5820T", - "T6022A", - "T6024A", - "T6027A", - "-6028T", - "-6029A", - "-6030A", - "-6031T", - "-6032A", - "A6034C", - "C6035A", - "A6036C", - "C6037G", - "G6039C", - "C6040T", - "T6043C", - "C6044A", - "A6046C", - "C6047A", - "A6048T", - "T6050G", - "G6051A", - "A6053-", - "C6458T", - "C6478T", - "C6518T", - "C6549T", - "T6669C", - "C6678T", - "C6777T", - "T6927C", - "G6938C", - "G6939A", - "A6941C", - "C7109T", - "G7343A", - "C7364A", - "G7391T", - "C7872T", - "A8558G", - "A8651G", - "C8936T", - "G10127A", - "C10449T", - "G10481A", - "T11558C", - "A12329G", - "T13339C" - ], - "G": [ - "A71V", - "P78S", - "P91L" - ], - "P": [ - "T89P" - ], - "SH": [ - "Y177K", - "N178K", - "-179*", - "-180*", - "T181H", - "A182G", - "S184Q" + "A630G", + "C4443T", + "A9104G" ] - }, - "labels": { - "aa": "G: A71V, P78S, P91L; P: T89P; SH: Y177K, N178K, -179*, -180*, T181H, A182G, S184Q" } } }, { - "name": "NODE_0000069", + "name": "PP947611", "node_attrs": { - "div": 0.146, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -13470,284 +12350,24 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1406T", - "C1725T", - "C2728T", - "A5063G", - "C5529T", - "T6653C", - "C7012-", - "A7014-", - "G7015-", - "G7016-", - "G7017-", - "A7019-", - "A7025-", - "G7026-", - "C7028-", - "C7030-", - "A7032-", - "T7033-", - "-7038A", - "-7043A", - "-7050A", - "-7051C", - "-7052A", - "-7053C", - "C7076T", - "T7817C" + "C8936T", + "G11980A" ], - "G": [ - "L136P" + "L": [ + "S1605N" ] }, "labels": { - "aa": "G: L136P" - } - }, - "children": [ - { - "name": "OP904127", - "node_attrs": { - "div": 0.149, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A882G", - "C1498A", - "C1724A", - "C2362T", - "A3070G", - "A3423T", - "T4964C", - "G5098A", - "A5557G", - "C5906T", - "C5965T", - "G6130A", - "C6225T", - "A6548C", - "T6550C", - "C6652T", - "T6972C", - "A6990-", - "A6991-", - "A6992-", - "C6993-", - "T6994-", - "A6995-", - "A6996-", - "A6997-", - "A6998-", - "T6999-", - "A7000-", - "T7001-", - "A7002-", - "A7003-", - "A7004-", - "T7005-", - "T7006-", - "T7007-", - "A7008-", - "G7009-", - "-7012A", - "-7014T", - "-7015A", - "-7016A", - "-7017A", - "-7019T", - "C7021T", - "-7023A", - "-7025T", - "-7026T", - "-7028G", - "-7030A", - "T7031C", - "-7032C", - "-7033A", - "-7034G", - "-7035G", - "-7036G", - "-7037A", - "-7039A", - "-7040C", - "-7041A", - "-7042T", - "-7044G", - "-7045A", - "-7046C", - "-7047A", - "-7048C", - "-7049T", - "A7055-", - "T7056-", - "T7095C", - "A7961G", - "A8627G", - "G10376A", - "T10890C", - "A10974C", - "A11309G", - "G12104A" - ], - "F": [ - "I7V" - ], - "G": [ - "N101T", - "S102P", - "P136S" - ], - "M2-1": [ - "S121N" - ], - "P": [ - "P84Q" - ], - "SH": [ - "T22A", - "T138I", - "H158Y" - ] - }, - "labels": { - "aa": "F: I7V; G: N101T, S102P, P136S; M2-1: S121N; P: P84Q; SH: T22A, T138I, H158Y" - } - } - }, - { - "name": "NODE_0000070", - "node_attrs": { - "div": 0.148, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A264G", - "A279G", - "A726G", - "A5942G", - "C6019T", - "T6489C", - "C6518T", - "A6525G", - "C6571A", - "C6623T", - "T6955C", - "C7013-", - "A7018-", - "A7020-", - "C7021-", - "A7022-", - "T7024-", - "A7027-", - "A7029-", - "T7031-", - "-7036C", - "-7037C", - "-7039G", - "-7040G", - "-7041G", - "-7042A", - "-7044A", - "-7045C", - "-7046A", - "-7047T", - "-7048A", - "-7049G", - "-7054C", - "G7058T", - "G7059A", - "T7269C", - "A7541G", - "C10094T", - "T10334C", - "C12143T" - ], - "G": [ - "P91L", - "P109T", - "P126L" - ], - "SH": [ - "K150R", - "L176F" - ] - }, - "labels": { - "aa": "G: P91L, P109T, P126L; SH: K150R, L176F" - } - }, - "children": [ - { - "name": "OP904138", - "node_attrs": { - "div": 0.149, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1582T", - "T4961C", - "G5072A", - "T5171C", - "T5265C", - "T5562C", - "C6282T", - "G6576A", - "G6719A", - "C6885T", - "G7655A", - "T10910C", - "A12393G" - ], - "G": [ - "G160E" - ], - "L": [ - "I1743V" - ], - "P": [ - "A112V" - ] - }, - "labels": { - "aa": "G: G160E; L: I1743V; P: A112V" - } - } - }, - { - "name": "OP904120", - "node_attrs": { - "div": 0.148, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + "aa": "L: S1605N" } - ] + } } ] }, { - "name": "NODE_0000071", + "name": "NODE_0000057", "node_attrs": { - "div": 0.147, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -13755,60 +12375,22 @@ "branch_attrs": { "mutations": { "nuc": [ - "A399G", - "A675G", - "G1532T", - "G1910A", - "T2087G", - "A2987G", - "C3309T", - "T4029C", - "T4080G", - "T4119C", - "C4963A", - "T5349C", - "T5403C", - "A5470T", - "T5473A", - "-5474A", - "-5475T", - "T5805C", - "T5945C", - "T6024A", - "-6028A", - "-6031A", - "G6038A", - "C6885T", - "A6998G", - "A8591G", - "T8969C", - "A10775G", - "G11918A", - "A12385C" - ], - "L": [ - "N1740T" - ], - "M2-1": [ - "T76N" - ], - "P": [ - "E95D" + "A2602G", + "G6483A" ], - "SH": [ - "L151S", - "Y177*" + "G": [ + "M79I" ] }, "labels": { - "aa": "L: N1740T; M2-1: T76N; P: E95D; SH: L151S, Y177*" + "aa": "G: M79I" } }, "children": [ { - "name": "OK644703", + "name": "PP947625", "node_attrs": { - "div": 0.151, + "div": 0.154, "clade_membership": { "value": "B1" } @@ -13816,146 +12398,71 @@ "branch_attrs": { "mutations": { "nuc": [ - "G12A", - "G1616A", - "C1658T", - "C1725T", - "C2212T", - "G3669A", - "C4185T", - "A4344G", - "G4428A", - "C5036T", - "C5246A", - "G6003A", - "C6019T", - "-6029A", - "-6030T", - "-6032A", - "A6033C", - "A6036G", - "C6037G", - "A6038C", - "G6039T", - "C6040T", - "T6042C", - "T6043A", - "C6044A", - "A6045C", - "C6047T", - "A6048-", - "T6049-", - "A6082G", - "A6503G", - "C6583T", - "C6694T", - "T6831C", + "T948C", + "A1670G", + "A1787G", + "T2257G", + "-6189C", + "-6190C", + "-6191A", + "-6192T", + "-6193A", + "-6194A", + "C6195T", + "C6196A", + "A6197C", + "T6198A", + "A6200T", + "T6201C", + "C6203A", + "A6204T", + "A6205G", + "T6206-", + "C6207-", + "A6208-", + "C6209-", + "T6210-", + "G6211-", + "A6212-", + "G6213A", + "T6214G", + "A6215T", + "-6217A", "T6865C", - "G6866A", - "G6938C", - "G6939A", - "A6941C", - "C7325T", - "C7535T", - "T7967A", - "G7970T", - "G8288A", - "T8378C", - "T8426C", - "T8511C", - "A9293T", - "G9296T", - "C10011T", - "G10463A", - "A10592G", - "G11717A", - "T12569C", - "A12575G", - "A13160G" + "T9182C", + "C11967T" ], "G": [ - "N86S", - "P113S", - "W207Q" + "W207R" ], - "M2-1": [ - "D170E" + "L": [ + "L1601F" ], - "SH": [ - "L176F", - "-179N", - "-180N", - "S184N" + "M": [ + "S31R" ] }, "labels": { - "aa": "G: N86S, P113S, W207Q; M2-1: D170E; SH: L176F, -179N, -180N, S184N" + "aa": "G: W207R; L: L1601F; M: S31R" } } }, { - "name": "NODE_0000072", + "name": "NODE_0000058", "node_attrs": { - "div": 0.148, + "div": 0.153, "clade_membership": { "value": "B1" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C753T", - "T6027A", - "-6029T", - "-6030A", - "-6032T", - "A6135G", - "C6518T", - "A6733T", - "A7748G", - "G10004A", - "A12140G", - "-13206T", - "-13208T", - "-13214A", - "-13215A", - "-13216T", - "-13217C", - "-13218T", - "T13221C", - "A13223C", - "T13224-", - "C13225-", - "T13226-", - "C13227-", - "A13228-", - "C13229-", - "A13230-", - "C13231A", - "A13232G", - "G13233C" - ], - "G": [ - "P91L", - "N165Y" - ], - "SH": [ - "N178K", - "-179I", - "-180I", - "A182Q", - "F183L" - ] - }, - "labels": { - "aa": "G: P91L, N165Y; SH: N178K, -179I, -180I, A182Q, F183L" - } + "mutations": {} }, "children": [ { - "name": "PP947701", + "name": "PP947615", "node_attrs": { - "div": 0.15, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -13963,44 +12470,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "G12A", - "T249C", - "G888A", - "T943C", - "A1457G", - "C2212T", - "A2361G", - "C2896T", - "A3198G", - "A4305G", - "C6512T", - "T6896C", - "A7988G", - "C8249T", - "A8582G", - "A8765G", - "G10691A", - "G12209A", - "-13207G", - "A13264G" - ], - "G": [ - "P89L", - "T145I" - ], - "M": [ - "N66S" + "C7856T" ] - }, - "labels": { - "aa": "G: P89L, T145I; M: N66S" } } }, { - "name": "NODE_0000073", + "name": "PP947605", "node_attrs": { - "div": 0.149, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -14008,378 +12486,20 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1233T", - "C1519T", - "G2485A", - "T2872C", - "G3537A", - "C5036T", - "A5631G", - "A6473T", - "A8486G", - "A8966G", - "A9110G", - "C9374T", - "C10679T", - "T12797C", - "-13207A" + "C4613T", + "A11848G" ], - "G": [ - "K76M" + "F": [ + "T521I" ], - "P": [ - "P91L" + "L": [ + "K1561R" ] }, "labels": { - "aa": "G: K76M; P: P91L" + "aa": "F: T521I; L: K1561R" } - }, - "children": [ - { - "name": "NODE_0000074", - "node_attrs": { - "div": 0.149, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T6831C" - ] - } - }, - "children": [ - { - "name": "PP947647", - "node_attrs": { - "div": 0.149, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C10121T", - "C12080T" - ] - } - } - }, - { - "name": "NODE_0000075", - "node_attrs": { - "div": 0.149, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A8273G", - "A10617G" - ], - "L": [ - "T1151A" - ] - }, - "labels": { - "aa": "L: T1151A" - } - }, - "children": [ - { - "name": "PP947684", - "node_attrs": { - "div": 0.15, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1991C", - "C3192T", - "T5591C", - "C6572T", - "A7004G", - "G7700A", - "A12440G" - ], - "G": [ - "P109L" - ], - "SH": [ - "V33A" - ] - }, - "labels": 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"children": [ { - "name": "PP947653", + "name": "NODE_0000065", "node_attrs": { - "div": 0.151, + "div": 0.15, "clade_membership": { "value": "B1" } @@ -14974,165 +13194,57 @@ "branch_attrs": { "mutations": { "nuc": [ - "A945G", - "C2762T", - "G3327A", - "G5204A", + "A399G", + "A675G", + "G1532T", + "G1910A", + "T2087G", + "A2987G", + "C3309T", + "T4029C", + "T4080G", + "T4119C", + "C4963A", + "T5349C", + "T5403C", "-5474A", "-5475T", - "C5743T", - "G6450A", - "T6806C", - "G6903A", - "G6914A", - "C6932T", - "G7067A", - "C7086A", - "C7139A", - "A8543G", - "A9425G", - "A9515G", - "A9858G", - "A9911G", - "T11027C", - "T11351C", - "C11977T", - "A12863G", - "G13337A" - ], - "G": [ - "M68I", - "I189T" + "T5805C", + "T5945C", + "-6028A", + "-6031A", + "G6038A", + "C6885T", + "A6998G", + "A8591G", + "T8969C", + "A10775G", + "G11918A", + "A12385C" ], "L": [ - "R898G", - "I915M", - "P1604L" - ], - "SH": [ - "P84S" - ] - }, - "labels": { - "aa": "G: M68I, I189T; L: R898G, I915M, P1604L; SH: P84S" 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"value": "B1" - } - }, - "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "NODE_0000085", - "node_attrs": { - "div": 0.146, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1677T", - "G4401A", - "T6942C", - "G8030A", - "A9455G", - "C11779T" - ], - "L": [ - "A1538V" + "L151S", + "Y177*" ] }, "labels": { - "aa": "L: A1538V" + "aa": "L: N1740T; M2-1: T76N; P: E95D; SH: L151S, Y177*" } }, "children": [ { - "name": "OP904077", + "name": "OK644703", "node_attrs": { - "div": 0.148, + "div": 0.154, "clade_membership": { "value": "B1" } @@ -15140,51 +13252,87 @@ "branch_attrs": { "mutations": { "nuc": [ - "C2177T", - "G2248A", - "C2923T", - "A3240G", - "C4158T", - "T4284C", - "C4991T", - "A5923G", - "C5934T", - "T6041C", - "A6155G", - "G6324A", - "C6504T", - "T6556C", - "T6645C", - "T6653C", - "C6678A", - "A7277C", - "G7784A", - "C8807T", - "C9056T", - "C9401T", - "T10653C", - "C12776T" + "G12A", + "G1616A", + "C1658T", + "C1725T", + "C2212T", + "G3669A", + "C4185T", + "A4344G", + "G4428A", + "C5036T", + "C5246A", + "G6003A", + "C6019T", + "-6029A", + "-6030T", + "-6032A", + "A6033C", + "A6036G", + "C6037G", + "A6038C", + "G6039T", + "C6040T", + "T6042C", + "T6043A", + "C6044A", + "A6045C", + "C6047T", + "A6048-", + "T6049-", + "A6082G", + "A6503G", + "C6583T", + "C6694T", + "T6831C", + "T6865C", + "G6866A", + "G6938C", + "G6939A", + "A6941C", + "C7325T", + "C7535T", + "T7967A", + "G7970T", + "G8288A", + "T8378C", + "T8426C", + "T8511C", + "A9293T", + "G9296T", + "C10011T", + "G10463A", + "A10592G", + "G11717A", + "T12569C", + "A12575G", + "A13160G" ], "G": [ - "F104L", - "L136P" + "N86S", + "P113S", + "W207Q" ], - "L": [ - "R37S" + "M2-1": [ + "D170E" ], "SH": [ - "T144A" + "L176F", + "-179N", + "-180N", + "S184N" ] }, "labels": { - "aa": "G: F104L, L136P; L: R37S; SH: T144A" + "aa": "G: N86S, P113S, W207Q; M2-1: D170E; SH: L176F, -179N, -180N, S184N" } } }, { - "name": "OP904041", + "name": "NODE_0000066", "node_attrs": { - "div": 0.147, + "div": 0.151, "clade_membership": { "value": "B1" } @@ -15192,80 +13340,103 @@ "branch_attrs": { "mutations": { "nuc": [ - "A675G", - "C1658T", - "T1745C", - "A1808G", - "G2284A", - "C2563T", - "A3552G", - "T4317C", - "G6085A", - "T6798C", - "G6938C", - "G6939A", - "A6941C", - "T6943C", - "A7736G", - "C8798T", - "A9941G", - "C10121T", - "T11321C", - "A11947G", - "C12381T" + "C753T", + "T6027A", + "-6029T", + "-6030A", + "-6032T", + "A6135G", + "C6518T", + "A6733T", + "A7748G", + "G10004A", + "A12140G", + "-13206T", + "-13208T", + "-13214A", + "-13215A", + "-13216T", + "-13217C", + "-13218T", + "T13221C", + "A13223C", + "T13224-", + "C13225-", + "T13226-", + "C13227-", + "A13228-", + "C13229-", + "A13230-", + "C13231A", + "A13232G", + "G13233C" ], - "L": [ - "K1594R" - ] - }, + "G": [ + "P91L", + "N165Y" + ], + "SH": [ + "N178K", + "-179I", + "-180I", + "A182Q", + "F183L" + ] + }, "labels": { - "aa": "L: K1594R" - } - } - } - ] - }, - { - "name": "NODE_0000086", - "node_attrs": { - "div": 0.146, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1044A", - "C6019T", - "A7418G", - "A9335G" - ], - "SH": [ - "L176F" - ] - }, - "labels": { - "aa": "SH: L176F" - } - }, - "children": [ - { - "name": "NODE_0000087", - "node_attrs": { - "div": 0.146, - "clade_membership": { - "value": "B1" + "aa": "G: P91L, N165Y; SH: N178K, -179I, -180I, A182Q, F183L" } }, - "branch_attrs": { - "mutations": {} - }, "children": [ { - "name": "NODE_0000088", + "name": "PP947701", + "node_attrs": { + "div": 0.152, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G12A", + "T249C", + "G888A", + "T943C", + "A1457G", + "C2212T", + "A2361G", + "C2896T", + "A3198G", + "A4305G", + "C6512T", + "T6896C", + "A7988G", + "C8249T", + "A8582G", + "A8765G", + "G10691A", + "G12209A", + "-13207G", + "A13264G" + ], + "G": [ + "P89L", + "T145I" + ], + "M": [ + "N66S" + ] + }, + "labels": { + "aa": "G: P89L, T145I; M: N66S" + } + } + }, + { + "name": "NODE_0000067", "node_attrs": { - "div": 0.147, + "div": 0.152, "clade_membership": { "value": "B1" } @@ -15273,18 +13444,38 @@ "branch_attrs": { "mutations": { "nuc": [ - "C7088G", - "A7089C", - "T7090A", - "C7091T" + "C1233T", + "C1519T", + "G2485A", + "T2872C", + "G3537A", + "C5036T", + "A5631G", + "A6473T", + "A8486G", + "A8966G", + "A9110G", + "C9374T", + "C10679T", + "T12797C", + "-13207A" + ], + "G": [ + "K76M" + ], + "P": [ + "P91L" ] + }, + "labels": { + "aa": "G: K76M; P: P91L" } }, "children": [ { - "name": "NODE_0000089", + "name": "NODE_0000068", "node_attrs": { - "div": 0.149, + "div": 0.152, "clade_membership": { "value": "B1" } @@ -15292,63 +13483,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1421T", - "G3081A", - "T3462C", - "C4287T", - "C4886T", - "G5123A", - "C5330T", - "G5706A", - "G5741A", - "C5745T", - "C6040T", - "C6682A", - "G6688A", - "A6689C", - "A6691C", - "C6693G", - "C6694A", - "A6695G", - "G6696A", - "G6698A", - "C6699A", - "A6701G", - "C6702A", - "C6705A", - "C6945T", - "T6972C", - "C7089T", - "G7338A", - "A8069G", - "A8525T", - "G9296A", - "A10533G", - "T11087C" - ], - "G": [ - "R155P" - ], - "L": [ - "V58I", - "I1123V" - ], - "M2-2": [ - "A28V" - ], - "SH": [ - "R83K" + "T6831C" ] - }, - "labels": { - "aa": "G: R155P; L: V58I, I1123V; M2-2: A28V; SH: R83K" } }, "children": [ { - "name": "OP904100", + "name": "PP947647", "node_attrs": { - "div": 0.149, + "div": 0.152, "clade_membership": { "value": "B1" } @@ -15356,23 +13499,16 @@ "branch_attrs": { "mutations": { "nuc": [ - "A541G", - "T5544C", - "A6687T" - ], - "N": [ - "I168V" + "C10121T", + "C12080T" ] - }, - "labels": { - "aa": "N: I168V" } } }, { - "name": "OP904081", + "name": "NODE_0000069", "node_attrs": { - "div": 0.149, + "div": 0.152, "clade_membership": { "value": "B1" } @@ -15380,23 +13516,79 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1351T" + "A8273G", + "A10617G" ], - "P": [ - "T35I" + "L": [ + "T1151A" ] }, "labels": { - "aa": "P: T35I" + "aa": "L: T1151A" } - } + }, + "children": [ + { + "name": "PP947684", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T1991C", + "C3192T", + "T5591C", + "C6572T", + "A7004G", + "G7700A", + "A12440G" + ], + "G": [ + "P109L" + ], + "SH": [ + "V33A" + ] + }, + "labels": { + "aa": "G: P109L; SH: V33A" + } + } + }, + { + "name": "PP947591", + "node_attrs": { + "div": 0.152, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G12087A" + ], + "L": [ + "D1641N" + ] + }, + "labels": { + "aa": "L: D1641N" + } + } + } + ] } ] }, { - "name": "NODE_0000090", + "name": "NODE_0000070", "node_attrs": { - "div": 0.147, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -15404,23 +13596,50 @@ "branch_attrs": { "mutations": { "nuc": [ - "T6489C", - "T6550C", - "A11573G" + 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"nuc": [ + "T1853C", + "A3843G", + "T4540C", + "G6718A", + "T6896C", + "A6905G", + "C7907T", + "T8051C", + "G10829A" + ], + "G": [ + "G160R" ] }, "labels": { - "aa": "SH: T120R" + "aa": "G: G160R" } }, "children": [ { - "name": "OP904038", + "name": "OP904123", "node_attrs": { - "div": 0.148, + "div": 0.151, "clade_membership": { "value": "B1" } @@ -16121,31 +14855,19 @@ "branch_attrs": { "mutations": { "nuc": [ - "C129T", - "A1364G", - "C5103T", - "G6797A", - "T10072C" - ], - "G": [ - "S186N" - ], - "L": [ - "L969S" - ], - "M2-1": [ - "H123Y" + "G900A", + "T3984C", + "A6191G", + "C6372T", + "T12803C" ] - }, - "labels": { - "aa": "G: S186N; L: L969S; M2-1: H123Y" } } }, { - "name": "NODE_0000099", + "name": "NODE_0000083", "node_attrs": { - "div": 0.148, + "div": 0.154, "clade_membership": { "value": "B1" } @@ -16153,44 +14875,73 @@ "branch_attrs": { "mutations": { "nuc": [ - "A3888T", - "C4174T", - "A7277G" + "A63G", + "A2934-", + "C2936A", + "T2937C", + "G2938T", + "T2939G", + 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"name": "PP947594", "node_attrs": { - "div": 0.15, + "div": 0.156, "clade_membership": { "value": "B1" } @@ -16198,28 +14949,20 @@ "branch_attrs": { "mutations": { "nuc": [ - "G99A", - "G885A", - "C1518T", - "T2942C", - "T2997C", - "C4158A", - "C5084T", - "C5322T", - "C6680T", - "G6688-", - "A6691C", - "C6694A", - "A6695G", - "G6696A", - "G6698A", - "C6699A", - "C6702A", - "A6703G", - "C6706A", - "C6707A", - "C6816T", - "G6858A", + "C1071T", + "A1508G", + "C1853T", + "G2230A", + "T2272C", + "T2965C", + "C3192T", + "C4540T", + "T5577C", + "A5862G", + "C5934T", + "C6500T", + "C6504T", + "C6588T", "C7012-", "C7013-", "A7014-", @@ -16245,7 +14988,7 @@ "-7037C", "-7038A", "-7039G", - "-7040A", + "-7040G", "-7041G", "-7042A", "-7043A", @@ -16261,169 +15004,34 @@ "-7053C", "-7054T", "G7058T", - "T7556C", - "G9890A", - "A10928G", - "A12029G", - "C12035A" + "G7059A", + "T7063G", + "T7064G", + "G7068C", + "C7069A", + "A7070C", + "C7071A", + "A7072T", + "T7073G", + "A7124T", + "G7125A", + "C9209T", + "A9722G", + "T9863C" ], "G": [ - "T144I", - "T145I", - "E146Q", - "K147T", - "K156A", - "R157T", - "E158T" - ], - "L": [ - "D1623E" - ], - "P": [ - "P91S" - ] - }, - "labels": { - "aa": "G: T144I, T145I, E146Q, K147T, K156A, R157T, E158T; L: D1623E; P: P91S" - } - } - } - ] - } - ] - }, - { - "name": "NODE_0000100", - "node_attrs": { - "div": 0.147, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G2530A", - "T3609C", - "A5388G", - "C6458T", - "T7122C", - "T8930C", - "T10646C", - "T12398C", - "T13061C" - ], - "G": [ - "A71V" - ] - }, - "labels": { - "aa": "G: A71V" - } - }, - "children": [ - { - "name": "OP904131", - "node_attrs": { - "div": 0.149, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1005T", - "C1829T", - "C2212T", - "T2983C", - "T3462C", - "T3486C", - "G3852A", - "A4760G", - "T4842C", - "T6624C", - "G6801A", - "C6824T", - "G7401A", - "C9245T", - "C9897T", - "T10385A", - "T11970A", - "C12776T" - ], - "G": [ - "P193L" - ], - "L": [ - "V79I", - "F1602I" - ] - }, - "labels": { - "aa": "G: P193L; L: V79I, F1602I" - } - } - }, - { - "name": "NODE_0000101", - "node_attrs": { - "div": 0.147, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C8936T" - ] - } - }, - "children": [ - { - "name": "OP904080", - "node_attrs": { - "div": 0.149, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1559C", - "G1598A", - "G2164A", - "G3033A", - "C3958T", - "C4128T", - "C4653T", - "A5030G", - "T6896C", - "G7015A", - "G7067A", - "A7405G", - "T7898C", - "C9161T", - "G9437A", - "T10895C", - "G12453A" - ], - "L": [ - "N80S", - "D1763N" + "P85L" ] }, "labels": { - "aa": "L: N80S, D1763N" + "aa": "G: P85L" } } }, { - "name": "NODE_0000102", + "name": "NODE_0000084", "node_attrs": { - "div": 0.149, + "div": 0.158, "clade_membership": { "value": "B1" } @@ -16431,49 +15039,95 @@ "branch_attrs": { "mutations": { "nuc": [ - "C78T", - "C2722T", - "C3102T", - "G3622A", - "C4443T", - "G4604A", - "T5895C", - "A6300G", - "G6578A", - "C6617T", - "G6911A", - "C6929T", - "G7472A", - "C9251T", - "A9447G", - "A10235C", - "A10346G", - "T13163C" - ], - "F": [ - "V191I", - "R518K" + "C546T", + "C949T", + "A1047G", + "A1376G", + "T1745C", + "A2102G", + "A2344G", + "G2482A", + "T2590C", + "T2957C", + "A4149G", + "A5355G", + "T5747C", + "G6009A", + "T6444C", + "T6653C", + "T6657C", + "A6688G", + "C6689A", + "C6691A", + "G6693C", + "A6694C", + "G6695A", + "A6696G", + "A6698G", + "A6699C", + "G6701A", + "A6702C", + "C6703A", + "A6705G", + "T6831C", + "A6841G", + "T6910C", + "G6938C", + "G6939A", + "A6941C", + "A7134G", + "T7178C", + "G8087A", + "C8249T", + "A8735G", + "T9680C", + "C9897T", + "T10163C", + "C10268A", + "G11063A" ], "G": [ - "I18M", - "G111D", - "T124I" + "L136P", + "S138K", + "T139S", + "H140T", + "E141H", + "Q142E", + "I143Q", + "Q145I", + "T146E", + "T147K", + "T156K", + "S157R", + "L158E", + "T199A" ], - "L": [ - "I761V" + "SH": [ + "I85T" ] }, "labels": { - "aa": "F: V191I, R518K; G: I18M, G111D, T124I; L: I761V" + "aa": "G: L136P, S138K, T139S, H140T, E141H, Q142E, I143Q, Q145I, T146E, T147K, T156K, S157R, L158E, T199A; SH: I85T" } }, "children": [ { - "name": "OP904104", + "name": "MW221995", "node_attrs": { - "div": 0.149, + "div": 0.158, + "accession": "MW221995", + "author": { + "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", + "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." + }, "clade_membership": { "value": "B1" + }, + "region": { + "value": "Oceania" + }, + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -16481,16 +15135,65 @@ } }, { - "name": "OP904079", + "name": "NODE_0000085", "node_attrs": { - "div": 0.149, + "div": 0.158, "clade_membership": { "value": "B1" } }, "branch_attrs": { - "mutations": {} - } + "mutations": { + "nuc": [ + "T5470A", + "A5473T", + "A5474-", + "T5475-", + "A6024T", + "A6027T", + "A6028-", + "T6029-", + "A6030-", + "A6031-", + "T6032-" + ], + "SH": [ + "*177Y", + "K178N", + "I179-", + "I180-" + ] + }, + "labels": { + "aa": "SH: *177Y, K178N, I179-, I180-" + } + }, + "children": [ + { + "name": "OP904160", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "OP904159", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": {} + } + } + ] } ] } @@ -16501,33 +15204,9 @@ ] } ] - } - ] - }, - { - "name": "NODE_0000103", - "node_attrs": { - "div": 0.146, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T6653C" - ], - "G": [ - "L136P" - ] }, - "labels": { - "aa": "G: L136P" - } - }, - "children": [ { - "name": "NODE_0000104", + "name": "NODE_0000086", "node_attrs": { "div": 0.149, "clade_membership": { @@ -16537,58 +15216,39 @@ "branch_attrs": { "mutations": { "nuc": [ - "A2934-", - "C2936A", - "T2937C", - "G2938T", - "T2939G", - "C2940T", - "T2941C", - "A2943T", - "T2945A", - "C2946T", - "A2947C", - "C2949A", - "A2950C", - "T2952A", - "G2954T", - "C2955G", - "T2957C", - "A2958T", - "T2959A", - "A2960T", - "T2961A", - "A2962T", - "C2964A", - "C2966T", - "T2967C", - "A2968T", - "G2969A", - "A2970G", - "G2971A", - "A2972G", - "T2973A", - "A2975T", - "T2977A", - "A2978T", - "G2980A", - "C2981G", - "T6896C", - "C13296T" + "G2120A", + "G5955A", + "C6943T", + "C7074G", + "A7075C", + "C7076A", + "A7078C", + "T7080A", + "G7081T", + "G7083A", + "A7084G", + "T7085A", + "G7086T", + "T8378C", + "T10211C" ], "G": [ - "R155P" + "T148-" + ], + "SH": [ + "M154I", + "S184N" ] }, "labels": { - "aa": "G: R155P" + "aa": "G: T148-; SH: M154I, S184N" } }, "children": [ { - "name": "NODE_0000105", + "name": "NODE_0000087", "node_attrs": { - "div": 0.155, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -16596,107 +15256,93 @@ "branch_attrs": { "mutations": { "nuc": [ - "C546T", - "C949T", - "A1044T", - "A1047G", - "C1358T", - "A1376G", - "C1633T", - "T1745C", - "T1853C", - "A2120G", - "A2344G", - "G2482A", - "T2590C", - "A3843G", - "A4149G", - "T4540C", - "A5355G", - "T5747C", - "A5955G", - "G6009A", - "T6019C", - "T6066C", - "A6135G", - "T6444C", - "A6657C", - "C6705G", - "G6718A", - "T6785C", + "T246C", + "C1466T", + "A1622G", + "G1649A", + "A1742G", + "C2045T", + "G3024A", + "C3096T", + "T3462C", + "A5470T", + "T5473A", + "A5976G", + "T6024A", + "T6027A", + "-6028T", + "-6029A", + "-6030A", + "-6031T", + "-6032A", + "A6034C", + "C6035A", + "A6036C", + "C6037G", + "G6039C", + "C6040T", + "T6043C", + "C6044A", + "A6046C", + "C6047A", + "A6048T", + "T6050G", + "G6051A", + "A6053-", + "T6454C", + "T6489C", + "T6557C", + "T6645C", + "C6650T", + "T6653C", + "A6713G", "T6831C", - "A6841G", - "A6905G", - "T6910C", - "G6938C", - "G6939A", - "A6941C", - "T6943C", - "G7074C", - "C7075A", - "A7076C", - "C7078A", - "A7080T", - "T7081G", - "A7083G", - "G7084A", - "A7085T", - "T7086G", - "C7109T", - "A7134G", - "T7178C", - "G7418A", - "C7466T", - "A7781G", - "C7907T", - "T8051C", - "G8087A", - "C8249T", - "C8378T", - "G8451A", - "A8735G", - "C9035T", - "G9335A", - "T9680C", - "C9897T", - "T10163C", - "C10211T", - "C10268A", - "G10829A", - "C11048T", - "G11063A", - "A11228G", - "A11615G", - "C12632T" + "A6986C", + "T7086C", + "T7889C", + "C7943T", + "A8273G", + "G8786A", + "C8936T", + "G9146A", + "A9347G", + "C11244T", + "G11918A", + "A12385G", + "A12701G", + "T13094C", + "A13124G", + "A13240G", + "C13249T", + "G13334A" ], "G": [ - "T145I", - "G160R", - "I182T", - "T199A" + "S70P", + "F104S", + "A135V", + "L136P", + "E158G" ], "L": [ - "A429T" - ], - "P": [ - "T129I" + "N1740S" ], "SH": [ - "I85T", - "I154M", - "F176L", - "A182R", - "F183L", - "N184S" + "Y177*", + "N178K", + "-179*", + "-180*", + "T181H", + "A182G", + "N184Q" ] }, "labels": { - "aa": "G: T145I, G160R, I182T, T199A; L: A429T; P: T129I; SH: I85T, I154M, F176L, A182R, F183L, N184S" + "aa": "G: S70P, F104S, A135V, L136P, E158G; L: N1740S; SH: Y177*, N178K, -179*, -180*, T181H, A182G, N184Q" } }, "children": [ { - "name": "OP904160", + "name": "PP947653", "node_attrs": { "div": 0.155, "clade_membership": { @@ -16704,85 +15350,126 @@ } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "A945G", + "C2762T", + "G3327A", + "G5204A", + "-5474A", + "-5475T", + "C5743T", + "G6450A", + "T6806C", + "G6903A", + "G6914A", + "C6932T", + "G7067A", + "C7086A", + "C7139A", + "A8543G", + "A9425G", + "A9515G", + "A9858G", + "A9911G", + "T11027C", + "T11351C", + "C11977T", + "A12863G", + "G13337A" + ], + "G": [ + "M68I", + "I189T" + ], + "L": [ + "R898G", + "I915M", + "P1604L" + ], + "SH": [ + "P84S" + ] + }, + "labels": { + "aa": "G: M68I, I189T; L: R898G, I915M, P1604L; SH: P84S" + } } }, { - "name": "NODE_0000106", + "name": "PP947586", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "B1" } }, "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "OP904159", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": {} - } + "mutations": { + "nuc": [ + "A306G", + "C1326T", + "T1520C", + "A1535G", + "C1709T", + "C2228T", + "C2287T", + "C2779T", + "T3120C", + "T3186C", + "C4104T", + "C4110T", + "G4131A", + "G4455A", + "G4470A", + "C4647T", + "T5379C", + "-5474T", + "-5475A", + "A5477G", + "A5479-", + "G5784A", + "T5896C", + "C5928T", + "G5935A", + "C6108A", + "-6110C", + "G6578A", + "C6596T", + "A6651G", + "C6852T", + "T7120C", + "A7694G", + "A8126G", + "T10068C", + "A10266G", + "C11501T", + "A11777G", + "C12080T", + "G13199T" + ], + "G": [ + "G111D", + "T117I" + ], + "L": [ + "I320M", + "I1034V" + ], + "SH": [ + "S135P", + "D148N" + ] }, - { - "name": "MW221995", - "node_attrs": { - "div": 0.155, - "accession": "MW221995", - "author": { - "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", - "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." - }, - "country": { - "value": "Australia" - }, - "region": { - "value": "Oceania" - }, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A5470T", - "T5473A", - "-5474A", - "-5475T", - "T6024A", - "T6027A", - "-6028A", - "-6029T", - "-6030A", - "-6031A", - "-6032T" - ], - "SH": [ - "Y177*", - "N178K", - "-179I", - "-180I" - ] - }, - "labels": { - "aa": "SH: Y177*, N178K, -179I, -180I" - } - } + "labels": { + "aa": "G: G111D, T117I; L: I320M, I1034V; SH: S135P, D148N" } - ] + } } ] }, { - "name": "NODE_0000107", + "name": "NODE_0000088", "node_attrs": { "div": 0.149, "clade_membership": { @@ -16790,17 +15477,13 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T2965C" - ] - } + "mutations": {} }, "children": [ { - "name": "OP904089", + "name": "NODE_0000089", "node_attrs": { - "div": 0.153, + "div": 0.149, "clade_membership": { "value": "B1" } @@ -16808,82 +15491,122 @@ "branch_attrs": { "mutations": { "nuc": [ - "C537T", - "C1020T", - "G1574A", - "T1577C", - "G1667A", - "G2845A", - "C2923T", - "A2952G", - "C3135T", - "T3462C", - "C3639T", - "T4242C", - "C4653T", - "T4982C", - "A5102G", - "G5201A", - "T5319C", - "C5393T", - "T5754C", - "T5944C", - "T6013C", - "C6037T", - "C6044T", - "A6357G", - "G6459A", - "T6489C", - "T6558C", - "T6582C", - "T6586C", - "C6623T", - "T6645C", - "T6669C", - "G6821A", - "C7088G", - "A7089C", - "T7090A", - "C7091T", - "G7338A", - "A7727G", - "G8321A", - "A8966G", - "G9833A", - "G10004A", - "A10050G", - "C10526T", - "A10676G", - "A11573G", - "G11717A", - "G12794A" - ], - "G": [ - "Y114H", - "P126L", - "E146G", - "R192K" + "C1677T", + "G4401A", + "T6942C", + "G8030A", + "A9455G", + "C11779T" ], "L": [ - "V58I", - "I962V" - ], - "M2-2": [ - "S49L" - ], - "SH": [ - "Y174H" + "A1538V" ] }, "labels": { - "aa": "G: Y114H, P126L, E146G, R192K; L: V58I, I962V; M2-2: S49L; SH: Y174H" + "aa": "L: A1538V" } - } + }, + "children": [ + { + "name": "OP904077", + "node_attrs": { + "div": 0.151, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C2177T", + "G2248A", + "C2923T", + "A3240G", + "C4158T", + "T4284C", + "C4991T", + "A5923G", + "C5934T", + "T6041C", + "A6155G", + "G6324A", + "C6504T", + "T6556C", + "T6645C", + "T6653C", + "C6678A", + "A7277C", + "G7784A", + "C8807T", + "C9056T", + "C9401T", + "T10653C", + "C12776T" + ], + "G": [ + "F104L", + "L136P" + ], + "L": [ + "R37S" + ], + "SH": [ + "T144A" + ] + }, + "labels": { + "aa": "G: F104L, L136P; L: R37S; SH: T144A" + } + } + }, + { + "name": "OP904041", + "node_attrs": { + "div": 0.151, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A675G", + "C1658T", + "T1745C", + "A1808G", + "G2284A", + "C2563T", + "A3552G", + "T4317C", + "G6085A", + "T6798C", + "G6938C", + "G6939A", + "A6941C", + "T6943C", + "A7736G", + "C8798T", + "A9941G", + "C10121T", + "T11321C", + "A11947G", + "C12381T" + ], + "L": [ + "K1594R" + ] + }, + "labels": { + "aa": "L: K1594R" + } + } + } + ] }, { - "name": "NODE_0000108", + "name": "NODE_0000090", "node_attrs": { - "div": 0.15, + "div": 0.149, "clade_membership": { "value": "B1" } @@ -16891,287 +15614,36 @@ "branch_attrs": { "mutations": { "nuc": [ - "G4749A", - "C6653T", - "A6990-", - "A6991-", - "A6992-", - "C6993-", - "T6994-", - "A6995-", - "A6996-", - "A6997-", - "A6998-", - "T6999-", - "A7000-", - "T7001-", - "A7002-", - "A7003-", - "A7004-", - "T7005-", - "T7006-", - "T7007-", - "A7008-", - "G7009-", - "C7012A", - "A7014T", - "G7015A", - "G7016A", - "G7017A", - "C7021T", - "-7023A", - "A7025T", - "G7026T", - "C7028G", - "C7030A", - "T7031C", - "A7032C", - "-7034G", - "-7035G", - "-7036G", - "-7037A", - "-7038A", - "-7039A", - "-7040C", - "-7041A", - "-7044G", - "-7045A", - "-7046C", - "-7047A", - "-7050A", - "-7051T", - "A7055-" - ], - 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} - } + "mutations": { + "nuc": [ + "C1351T" + ], + "P": [ + "T35I" ] + }, + "labels": { + "aa": "P: T35I" } - ] + } } ] - } - ] - }, - { - "name": "NODE_0000127", - "node_attrs": { - "div": 0.151, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A237C", - "G5048A", - "A5746G", - "T6582C", - "T6669C", - "T6798C", - "A6906C", - "A6984-", - "A6985-", - "A6986-", - "C6987-", - "C6988-", - "A6989-", - "-6996C", - "-6998C", - "-6999C", - "-7001A", - "-7004C", - "-7006A", - "A7010-", - "A7011-", - "C7013-", - "T7014-", - "A7018T", - "A7020T", - "T7021A", - "-7045A", - "-7054A", - "-7055A", - "-7056G", - "A7057G", - "G7058-", - "G7059-", - "G7060-", - "A7688G", - "A11870G" - ], - "SH": [ - "I85V" - ] }, - "labels": { - "aa": "SH: I85V" - } - }, - "children": [ { - "name": "NODE_0000128", + "name": "NODE_0000102", "node_attrs": { - "div": 0.151, + "div": 0.15, "clade_membership": { "value": "B1" } @@ -18755,114 +16342,14 @@ "branch_attrs": { "mutations": { "nuc": [ - "A5557C", - "C5558A", - "A5560T", - "T5562A" - ], - "SH": [ - "T22Q", - "I23L" + "T6489C", + "A11573G" ] - }, - "labels": { - "aa": "SH: T22Q, I23L" } }, "children": [ { - "name": "PP947569", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A273G", - "A447G", - "G1205A", - "T1552C", - "C1580T", - "A1871G", - "G2164A", - "A2424G", - "A2503G", - "C2878T", - "C3474T", - "T4206C", - "A5477G", - "T5739C", - "T5823C", - "G6126A", - "C6153T", - "T6156C", - "C6189-", - "C6190-", - "A6191-", - "T6192-", - "A6193-", - "A6194-", - "T6195C", - "-6196C", - "T6201-", - "C6202T", - "C6204T", - "T6205A", - "G6206A", - "A6207T", - "G6208C", - "T6209A", - "-6210C", - "-6211T", - "-6212G", - "-6213A", - "-6214G", - "-6215C", - "A6598T", - "T6600C", - "C6965A", - "C7075A", - "C7250T", - "A7600G", - "C8807T", - "G9137A", - "C9161T", - "G9305T", - "T9653C", - "C9773T", - "G9797A", - "T10493C", - 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"children": [ { - "name": "PP947583", + "name": "OP904132", "node_attrs": { - "div": 0.154, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -18902,73 +16409,28 @@ "branch_attrs": { "mutations": { "nuc": [ - "C354T", - "C843T", - "C1014T", - "C1038T", - "A2424G", - "A2743G", - "T3247C", - "C3778T", - "C4653T", - "G4892A", - "T5265C", - "T5442C", - "G6345A", - "A6691C", - "C6693G", - "A6695G", - "G6696A", - "A6701G", - "A6703C", - "C6823T", - "C6965A", - "C6996T", - "T7042C", - "C7109T", - "T7158C", - "G7418A", - "T7880C", - "C7934T", - "G8767A", - "G8786A", - "G8825A", - "C8936T", - "C9245T", - "C9614T", - "T11576C", - "T12404C", - "G12824A" + "T1853C", + "T3999C", + "T6550C", + "T6556C", + "G6561A", + "T6586C" ], "G": [ - "K138S", - "S139T", - "T140H", - "H141E", - "E142Q", - "Q143I", - "T145Q", - "E146T", - "R155A", - "E158S", - "P193S" - ], - "L": [ - "R534H" - ], - "M": [ - "K87R" + "S102P", + "F104L", + "Y114H" ] }, "labels": { - "aa": "G: K138S, S139T, T140H, H141E, E142Q, Q143I, T145Q, E146T, R155A, E158S, P193S; L: R534H; M: K87R" + "aa": "G: S102P, F104L, Y114H" } } }, { - "name": "OP904019", + "name": "NODE_0000104", "node_attrs": { - "div": 0.158, + "div": 0.153, "clade_membership": { "value": "B1" } @@ -18976,239 +16438,343 @@ "branch_attrs": { "mutations": { "nuc": [ - "A306G", - "A359G", - "A1089G", - "T1152C", - "A2123G", - "C2126T", - "T2258C", - "T2365C", - "C3028T", - "C3405T", - "G4904A", - "T5135C", - "G5367A", - "T5470A", - "A5473T", - "A5474-", - "T5475-", - "A5526G", - "A6024T", - "A6028-", - "A6029-", - "T6030-", - "A6031-", - "A6032-", - "C6033A", - "G6036A", - "G6037C", - "C6038G", - "T6039G", - "T6040C", - "C6042T", - "A6043T", - "A6044C", - "C6045A", - "T6047C", - "-6048A", - "-6049T", - "C6143T", - "A6692C", - "C6693A", - "A6694G", - "A6702G", - "A6704C", - "C6706A", - "A6708C", - "G6711A", - "A6713C", - "G6716C", - "G6718A", - "G6719C", - "G6720C", - "A6721C", - "A6722C", - "G6724A", - "C6729G", - "A6730G", - "C6731A", - 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"C6047T", + "A6048-", + "T6049-" + ], + "SH": [ + "Y177*", + "-179N", + "-180N" + ] + }, + "labels": { + "aa": "SH: Y177*, -179N, -180N" + } + }, + "children": [ + { + "name": "PP947662", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T5807C", + "C5808A", + "T5810A", + "A5812G", + "T6557C", + "T6624C", + "T6645C", + "T6806C", + "T6831C", + "T6865C", + "C6946T", + "A7895G", + "G10865A", + "C12095T" + ], + "G": [ + "F104S", + "I189T", + "W207R" + ], + "SH": [ + "I106T" + ] + }, + "labels": { + "aa": "G: F104S, I189T, W207R; SH: I106T" + } + } + }, + { + "name": "PP947593", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T249C", + "C1137T", + "T3005A", + "A3006T", + "-3009A", + "C6153T", + "C6558T", + "C6588T", + "C6623T", + "C7012-", + "C7013-", + "A7014-", + "G7015-", + "G7016-", + "G7017-", + "A7018-", + "A7019-", + 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"nuc": [ + "C6588T", + "C6623T" + ], + "G": [ + "P126L" + ] + }, + "labels": { + "aa": "G: P126L" + } + }, + "children": [ + { + "name": "OP904149", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G1119A", + "G2090A", + "C3345T", + "T3657C", + "A4265G", + "A4344G", + "T4389C", + "A5661G", + "A6164-", + "G6165-", + "T6166-", + "C6167-", + "A6168-", + "C6171T", + "C6174A", + "T6175-", + "G6176A", + "T6178C", + "G6179A", + "A6181T", + "A6182G", + "A6183C", + "C6184T", + "T6185G", + "T6188A", + "C6189A", + "A6191T", + "T6192C", + "A6194T", + "T6195C", + "-6196C", + "T6201-", + "C6202T", + "C6204T", + "T6205A", + "G6206A", + "A6207T", + "G6208C", + "T6209A", + "-6210C", + "-6211T", + "-6212G", + "-6213A", + "-6214G", + "-6215T", + "C6494T", + "T6550C", + "T6645C", + "T6653C", + "T6669C", + "A7101G", + "A8439G", + "A10578G", + "G10865A", + "C12336T" + ], + "F": [ + "K405R" + ], + "G": [ + "A83V", + "S102P", + "L136P" + ], + "L": [ + "S425G", + "N1138D", + "L1724F" + ] + }, + "labels": { + "aa": "F: K405R; G: A83V, S102P, L136P; L: S425G, N1138D, L1724F" + } + } + }, + { + "name": "OP904129", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "B1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T930C", + "T943C", + "C3826T", + "A6150G", + "C6558T", + "A8606G", + "A10055T", + "C12206T", + "T12881G" + ] + } + } + } ] - }, - "labels": { - "aa": "G: T144I, E146Q, -148T, T156A, E158T, T173I, P214-; L: R963Q; N: K107R; SH: *177Y, N179-, N180-" } - } - } - ] - } - ] - }, - { - "name": "NODE_0000130", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C2936T", - "T5135C", - "C6572T", - "C6758T", - "T7117C", - "G7391A", - "A7868G", - "A8273G", - "G8666A", - "C9367A", - "T9956C", - "T10199C", - "G10706A", - "C10838T", - "A11700G", - "G13106A" - ], - "G": [ - "P109L", - "T173I" - ], - "L": [ - "T734N", - "I1512V" - ] - }, - "labels": { - "aa": "G: P109L, T173I; L: T734N, I1512V" - } - }, - "children": [ - { - "name": "PP947568", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "B1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T681C", - "A954G", - "T990C", - "C1005A", - "T1186C", - "A1754G", - "C2326T", - "G3558A", - "A4446G", - "A4612G", - "T4673C", - "A5083G", - "C5174T", - "-6110A", - "G6114-", - "G6280A", - "G6577A", - "C6741T", - "A6835G", - "G6848A", - "T6877C", - "T6942C", - "C6965A", - "G8060A", - "A8495G", - "C8972T", - "T9029C", - "C9518T", - "A9830G", - "C10550T", - "C11096T", - "A11604G", - "T12170C", - "G12629A", - "T13248C" - ], - "F": [ - "T521A" - ], - "G": [ - "D12N", - "G111S", - "T197A", - "S201N", - "S211P" - ], - "L": [ - "I1480V" - ], - "M2-1": [ - "N116S" ] - }, - "labels": { - "aa": "F: T521A; G: D12N, G111S, T197A, S201N, S211P; L: I1480V; M2-1: N116S" } - } + ] }, { - "name": "NODE_0000131", + "name": "NODE_0000107", "node_attrs": { - "div": 0.156, + "div": 0.15, "clade_membership": { "value": "B1" } @@ -19216,100 +16782,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1445A", - "A1468G", - "C4581T", - "T5470A", - "A5473T", - "A5474-", - "T5475-", - "A5655G", - "C5749G", - "A5894G", - "C5934T", - "A6024T", - "A6028-", - "A6029-", - "T6030-", - "A6031-", - "A6032-", - "C6033A", - "G6036A", - "G6037C", - "C6038G", - "T6039G", - "T6040C", - "C6042T", - "A6043T", - "A6044C", - "C6045A", - "T6047C", - "-6048A", - "-6049T", - "T6091C", - "A6164-", - "G6165-", - "T6166-", - "C6167-", - "A6168-", - "C6171T", - "C6174A", - "T6175-", - "G6176A", - "T6178C", - "G6179A", - "A6181T", - "A6182G", - "A6183C", - "C6184T", - "T6185G", - "T6188A", - "C6189A", - "A6191T", - "T6192C", - "A6194T", - "T6195C", - "-6196C", - "T6201-", - "C6202T", - "C6204T", - "T6205A", - "G6206A", - "A6207T", - "G6208C", - "T6209A", - "-6210C", - "-6211T", - "-6212G", - "-6213A", - "-6214G", - "-6215T", - "C6816T", - "A8219G", - "C8936T", - "G9581A", - "A12554G" - ], - "P": [ - "N74S" - ], - "SH": [ - "P86A", - "N134S", - "*177Y", - "N179-", - "N180-" + "T6896C" ] - }, - "labels": { - "aa": "P: N74S; SH: P86A, N134S, *177Y, N179-, N180-" } }, "children": [ { - "name": "OP904023", + "name": "OP904150", "node_attrs": { - "div": 0.156, + "div": 0.155, "clade_membership": { "value": "B1" } @@ -19317,21 +16798,100 @@ "branch_attrs": { "mutations": { "nuc": [ - "G356A" + "A326G", + "A393T", + "G609A", + "A723G", + "A1331G", + "A1622G", + "A1643G", + "G2090A", + "G2164A", + "T2452C", + "G2482A", + "T2509G", + "C3096T", + "C3462T", + "A4062G", + "G4131T", + "C4203T", + "T5668C", + "G5673A", + "G5974A", + "C5985T", + "C6040T", + "A6222T", + "C6318T", + "T6444C", + "A6548G", + "T6550C", + "T6557C", + "T6559C", + "C6560T", + "A6568G", + "T6624C", + "T6653C", + "T6669C", + "A6708C", + "A6725G", + "T6785C", + "T6798C", + "G6827A", + "C6923A", + "G6938C", + "G6939A", + "A6941C", + "T6942C", + "C7471T", + 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"A8990G", + "A9020G", + "T9072C", + "G9080A", + "G9146T", + "A9149G", + "C9161T", + "T9191C", + "A9233G", + "A9272G", + "T9273C", + "A9335G", + "G9362T", + "C9371T", + "A9497G", + "G9560A", + "T9617C", + "A9635G", + "A9701G", + "A9716G", + "C9800T", + "G9815A", + "A9821G", + "T9843C", + "G9857A", + "A9869G", + "T9935C", + "C9974T", + "A9983G", + "G10022T", + "A10025G", + "C10034T", + "C10061T", + "T10124C", + "A10130G", + "A10139G", + "C10143A", + "C10187T", + "C10220T", + "T10301C", + "G10304A", + "C10305T", "C10370T", "A10394G", "C10514T", @@ -19829,19 +19758,17 @@ "T10607A", "T10920C", "T10973C", - "C11009T", "T11027C", "G11255A", - "C11330T", "G11438A", "A11457G", - "T11483C", - "G11585A", - "A11768G", + "G11795A", "T11801C", "A11822G", + "T11826C", "T11841C", "G11885A", + "A11998G", "T12014C", "A12029G", "A12048G", @@ -19849,54 +19776,57 @@ "A12140G", "T12173A", "T12191C", - "T12230C", "A12236G", "A12293G", - "T12302C", "C12335T", + "C12381T", "A12399G", "A12422G", "A12443G", "G12536A", + "T12628C", "A12662G", "A12749G", - "C12752A", - "G12824A", + "T12752A", + "T12807C", + "G12818A", "T12881A", "G12893A", "T12915C", - "C12935T", "T12944C", "T13031C", "C13154T", "T13157C", "G13199A", - "T13202C", + "A13207-", "A13235G", + "G13252A", "T13257C", - "-13279A" + "-13278T" ], "F": [ "Q143T", "N296D" ], "G": [ + "I18M", "T62V", "A66V", - "S70P", "A71V", "T82A", "A83V", "P85L", "W97L", + "N101D", "G111D", + "Y114H", + "T123A", "A125V", "K132E", "E142R", + "R155G", "R161K", "S186T", - "D191A", - "T195N", "T197A", "E203D", "R207Q", @@ -19919,35 +19849,38 @@ "E531D", "I537T", "I608M", + "I1431V", "S1559P", "N1611S", "I1628V", "S1745G", + "V1821T", "Y1881H" ], "P": [ "K29R", - "N74S", + "A85T", "F97L", "L103S", + "F118S", "S119P" ], "SH": [ - "T22I", "V30L", "S64L", "V90A", "R100K", - "S108D", "K116T", + "I133M", + "G137N", "A145V", "V155T", "G172W", - "I180K" + "-179E" ] }, "labels": { - "aa": "F: Q143T, N296D; G: T62V, A66V, S70P, A71V, T82A, A83V, P85L, W97L, G111D, A125V, K132E, E142R, R161K, S186T, D191A, T195N, T197A, E203D, R207Q, T209A, T229D, T231S, L233P, S235-; L: N42K, V79I, N113S, L238F, C262S, V307M, A429V, T496I, A505V, E531D, I537T, I608M, S1559P, N1611S, I1628V, S1745G, Y1881H; P: K29R, N74S, F97L, L103S, S119P; SH: T22I, V30L, S64L, V90A, R100K, S108D, K116T, A145V, V155T, G172W, I180K", + "aa": "F: Q143T, N296D; G: I18M, T62V, A66V, A71V, T82A, A83V, P85L, W97L, N101D, G111D, Y114H, T123A, A125V, K132E, E142R, R155G, R161K, S186T, T197A, E203D, R207Q, T209A, T229D, T231S, L233P, S235-; L: N42K, V79I, N113S, L238F, C262S, V307M, A429V, T496I, A505V, E531D, I537T, I608M, I1431V, S1559P, N1611S, I1628V, S1745G, V1821T, Y1881H; P: K29R, A85T, F97L, L103S, F118S, S119P; SH: V30L, S64L, V90A, R100K, K116T, I133M, G137N, A145V, V155T, G172W, -179E", "clade": "B2" } }, @@ -19955,7 +19888,7 @@ { "name": "NODE_0000134", "node_attrs": { - "div": 0.113, + "div": 0.112, "clade_membership": { "value": "B2" } @@ -19964,21 +19897,8 @@ "mutations": { "nuc": [ "G3519A", - "A6692C", - "A6694G", - "C6702G", - "A6704C", - "C6706A", - "G6708C", - "G6711A", - "A6712G", - "A6720C", - "G6724A", - "A6727G", - "A6732C", "C6735A", "A6738T", - "A6739C", "C6740G", "T6741A", "A6744C", @@ -19990,18 +19910,15 @@ "T6759A", "C6760A", "A6761C", - "A6762C", "A6763C", "C6764A", "G6832A", "G12704A" ], "G": [ - "S138R", "T153P", "K161E", "E162T", - "R166T", "T168S", "S169T", "T170A", @@ -20016,14 +19933,14 @@ ] }, "labels": { - "aa": "G: S138R, T153P, K161E, E162T, R166T, T168S, S169T, T170A, A172T, T173Q, Q174T, T178Q, N180S, N184E, E187T, T189-" + "aa": "G: T153P, K161E, E162T, T168S, S169T, T170A, A172T, T173Q, Q174T, T178Q, N180S, N184E, E187T, T189-" } }, "children": [ { "name": "FJ168778", "node_attrs": { - "div": 0.12, + "div": 0.119, "clade_membership": { "value": "B2" } @@ -20038,7 +19955,6 @@ "A597G", "C610T", "A807G", - "C894T", "G915A", "A1056G", "A1859G", @@ -20093,6 +20009,7 @@ "C12851T", "A13155C", "C13157T", + "C13206-", "A13214-", "A13215-", "T13216-", @@ -20141,7 +20058,6 @@ "T98A", "T99A", "H133Y", - "R155G", "Q181Y", "T182V" ], @@ -20155,14 +20071,14 @@ ] }, "labels": { - "aa": "G: T55M, T98A, T99A, H133Y, R155G, Q181Y, T182V; L: T537L, I856M, T1997P; M2-1: D85N" + "aa": "G: T55M, T98A, T99A, H133Y, Q181Y, T182V; L: T537L, I856M, T1997P; M2-1: D85N" } } }, { "name": "NODE_0000135", "node_attrs": { - "div": 0.121, + "div": 0.12, "clade_membership": { "value": "B2" } @@ -20173,6 +20089,7 @@ "T300C", "T669C", "A888G", + "T894C", "T987C", "A1493G", "G1551A", @@ -20268,7 +20185,6 @@ "C12411T", "T12758C", "C13091T", - "-13206C", "-13207A", "-13208T", "A13230G" @@ -20282,6 +20198,7 @@ "Q93R", "S109L", "T149A", + "G155R", "Q181N", "T182G", "S196N" @@ -20295,14 +20212,14 @@ ] }, "labels": { - "aa": "F: R450K; G: T39S, L56S, Q93R, S109L, T149A, Q181N, T182G, S196N; P: V102I; SH: I114V, L183F" + "aa": "F: R450K; G: T39S, L56S, Q93R, S109L, T149A, G155R, Q181N, T182G, S196N; P: V102I; SH: I114V, L183F" } }, "children": [ { "name": "NODE_0000136", "node_attrs": { - "div": 0.126, + "div": 0.125, "clade_membership": { "value": "B2" } @@ -20400,20 +20317,20 @@ { "name": "KF530170", "node_attrs": { - "div": 0.129, + "div": 0.128, "accession": "KF530170", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B2" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -20498,7 +20415,7 @@ { "name": "NODE_0000137", "node_attrs": { - "div": 0.126, + "div": 0.125, "clade_membership": { "value": "B2" } @@ -20522,14 +20439,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B2" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -20583,20 +20500,20 @@ { "name": "KC562231", "node_attrs": { - "div": 0.134, + "div": 0.133, "accession": "KC562231", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B2" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -20811,7 +20728,7 @@ { "name": "NODE_0000138", "node_attrs": { - "div": 0.121, + "div": 0.12, "clade_membership": { "value": "B2" } @@ -20837,7 +20754,7 @@ { "name": "NODE_0000139", "node_attrs": { - "div": 0.122, + "div": 0.121, "clade_membership": { "value": "B2" } @@ -20874,14 +20791,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "B2" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -21025,7 +20942,7 @@ { "name": "PP947686", "node_attrs": { - "div": 0.138, + "div": 0.137, "clade_membership": { "value": "B2" } @@ -21310,7 +21227,7 @@ { "name": "NODE_0000140", "node_attrs": { - "div": 0.124, + "div": 0.123, "clade_membership": { "value": "B2" } @@ -21404,20 +21321,20 @@ { "name": "KC562228", "node_attrs": { - "div": 0.124, + "div": 0.123, "accession": "KC562228", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -21449,7 +21366,7 @@ { "name": "NODE_0000141", "node_attrs": { - "div": 0.124, + "div": 0.123, "clade_membership": { "value": "B2" } @@ -21461,20 +21378,20 @@ { "name": "KC562232", "node_attrs": { - "div": 0.124, + "div": 0.123, "accession": "KC562232", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -21498,7 +21415,7 @@ { "name": "NODE_0000142", "node_attrs": { - "div": 0.126, + "div": 0.125, "clade_membership": { "value": "B2" } @@ -21563,14 +21480,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -21629,20 +21546,20 @@ { "name": "JN184402", "node_attrs": { - "div": 0.128, + "div": 0.127, "accession": "JN184402", "author": { "author": "Piyaratna,R.,Tollefson,S.J.,Williams,J.V.,Piyaratna,R.V.", "value": "Piyaratna,R.,Tollefson,S.J.,Williams,J.V.,Piyaratna,R.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -21736,7 +21653,7 @@ { "name": "NODE_0000143", "node_attrs": { - "div": 0.114, + "div": 0.113, "clade_membership": { "value": "B2" } @@ -21754,24 +21671,17 @@ "C6512T", "C6633T", "C6665T", - "A6691C", - "A6693G", - "A6695G", - "G6696A", - "A6701G", - "G6710A", - "A6717C", - "C6719A", - "A6730G", "C6731A", + "C6732A", + "C6739A", "A6742C", "C6743G", "C6752G", "G6754A", + "C6762A", "A6766C", "C6767T", "G6848A", - "T7533C", "C8370T", "A8867G", "A8870G", @@ -21797,9 +21707,9 @@ "T158K", "K160E", "R165T", + "T166R", "T176L", "R183S", - "A185G", "T186R", "S196G" ], @@ -21808,7 +21718,7 @@ ] }, "labels": { - "aa": "G: P89L, S139I, T140N, N141R, R142Q, Q143T, T145Q, Q146T, A156T, T158K, K160E, R165T, T176L, R183S, A185G, T186R, S196G; L: I761T" + "aa": "G: P89L, S139I, T140N, N141R, R142Q, Q143T, T145Q, Q146T, A156T, T158K, K160E, R165T, T166R, T176L, R183S, T186R, S196G; L: I761T" } }, "children": [ @@ -21825,6 +21735,7 @@ "nuc": [ "C15A", "C252T", + "T894C", "T1017C", "A1047G", "C1440T", @@ -21856,7 +21767,27 @@ "C6477T", "T6584C", "A6634G", + "A6691C", + "C6692A", + "A6693G", + "G6694A", + "A6695G", + "G6696A", + "A6701G", + "G6702C", + "C6704A", + "A6706C", + "C6708G", + "G6710A", + "A6711G", + "G6712A", + "A6717C", + "C6719A", + "C6720A", + "A6724G", + "G6727A", "A6729G", + "A6730G", "C6747T", "A6762G", "A6805G", @@ -21864,6 +21795,7 @@ "G7070A", "A7289G", "G7373A", + "T7533C", "C7850T", "G8451A", "T8776C", @@ -21881,7 +21813,6 @@ "T12680C", "C12692T", "C13118T", - "-13206C", "-13207A", "-13208T" ], @@ -21892,6 +21823,8 @@ "T55I", "L113P", "T130A", + "R138S", + "A185G", "T188A", "T189A", "S201N", @@ -21900,7 +21833,7 @@ "S213R", "S215K", "T219Y", - "T224N", + "-224N", "-225N" ], "L": [ @@ -21917,14 +21850,14 @@ ] }, "labels": { - "aa": "F: T504A; G: T55I, L113P, T130A, T188A, T189A, S201N, E210P, P211G, S213R, S215K, T219Y, T224N, -225N; L: S123P, V429I, K538R, T1620A; M: T108A; M2-2: D30N" + "aa": "F: T504A; G: T55I, L113P, T130A, R138S, A185G, T188A, T189A, S201N, E210P, P211G, S213R, S215K, T219Y, -224N, -225N; L: S123P, V429I, K538R, T1620A; M: T108A; M2-2: D30N" } }, "children": [ { "name": "NODE_0000145", "node_attrs": { - "div": 0.119, + "div": 0.12, "clade_membership": { "value": "B2" } @@ -21940,20 +21873,20 @@ { "name": "KC403972", "node_attrs": { - "div": 0.119, + "div": 0.12, "accession": "KC403972", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -22008,14 +21941,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": 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"Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -22165,20 +22098,20 @@ { "name": "KC562229", "node_attrs": { - "div": 0.122, + "div": 0.123, "accession": "KC562229", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -22256,20 +22189,20 @@ { "name": "KC562239", "node_attrs": { - "div": 0.121, + "div": 0.122, "accession": "KC562239", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -22317,14 +22250,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "B2" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -22340,7 +22273,7 @@ { "name": "NODE_0000150", "node_attrs": { - "div": 0.125, + "div": 0.124, "clade_membership": { "value": "B2" } @@ -22355,7 +22288,6 @@ "T666C", "G768A", "T883C", - "C894T", "C1122T", "T1144C", "T1358C", @@ -22368,7 +22300,6 @@ "T1769C", "T1806C", "A2194G", - "C2473T", "C2773A", "C2956T", "C3102T", @@ -22452,7 +22383,7 @@ "A7292G", "G7329A", "T7432C", - "C7533A", + "T7533A", "G7574A", "A7736G", "G7758A", @@ -22502,6 +22433,7 @@ "C12962T", "A13196C", "C13205-", + "C13206-", "-13210T", "-13211C", "-13212A", @@ -22517,11 +22449,8 @@ "D111N", "V125I", "T129A", - "T149E", "E150K", - "T154G", - "R155A", - "G185R", + "A185R", "S201Q", "S202N", "D203S", @@ -22565,14 +22494,14 @@ ] }, "labels": { - "aa": "F: T223N, D280N, I392T, R396Q; G: D111N, V125I, T129A, T149E, E150K, T154G, R155A, G185R, S201Q, S202N, D203S, Q204D, T205Q, P214G, H223T, -226A, N227H, T228N, D229A, T230D, S231T, P233S, S234L, -235S; L: V55I, I89T, S123T, V198I, T537I, G760S, I856M, T960A; M2-1: S121N; P: N44T, L64P, K109R; SH: E14K, K25N, T138A, H158Y" + "aa": "F: T223N, D280N, I392T, R396Q; G: D111N, V125I, T129A, E150K, A185R, S201Q, S202N, D203S, Q204D, T205Q, P214G, H223T, -226A, N227H, T228N, D229A, T230D, S231T, P233S, S234L, -235S; L: V55I, I89T, S123T, V198I, T537I, G760S, I856M, T960A; M2-1: S121N; P: N44T, L64P, K109R; SH: E14K, K25N, T138A, H158Y" } }, "children": [ { "name": "NODE_0000151", "node_attrs": { - "div": 0.125, + "div": 0.124, "clade_membership": { "value": "B2" } @@ -22582,7 +22511,7 @@ "nuc": [ "G2527A", "C6607T", - "A6720T", + "C6720T", "C6852T", "T6925C", "G8282A" @@ -22617,14 +22546,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "B2" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -22635,6 +22564,7 @@ "G966A", "T990C", "A1844G", + "C2473T", "C3106T", "T3342C", "G3912A", @@ -22667,6 +22597,25 @@ "G6430A", "T6549C", "T6584C", + "A6691C", + "C6692A", + "A6693G", + "G6694A", + "A6695G", + "G6696A", + "A6701G", + "G6702C", + "C6704A", + "A6706C", + "C6708G", + "G6710A", + "A6711G", + "G6712A", + "A6717C", + "C6719A", + "A6724G", + "G6727A", + "A6730G", "G6875A", "C6877T", "A6888G", @@ -22717,6 +22666,7 @@ "R4K", "V62M", "L113P", + "R138S", "K158N" ], "L": [ @@ -22728,14 +22678,14 @@ ] }, "labels": { - "aa": "G: R4K, V62M, L113P, K158N; L: I496N; SH: V91A, K126E" + "aa": "G: R4K, V62M, L113P, R138S, K158N; L: I496N; SH: V91A, K126E" } } }, { "name": "NODE_0000152", "node_attrs": { - "div": 0.128, + "div": 0.125, "clade_membership": { "value": "B2" } @@ -22744,52 +22694,31 @@ "mutations": { "nuc": [ "A1107G", - "T2473C", - "C6691A", - "A6692C", - "G6693A", - "A6694G", - "G6695A", - "A6696G", - "G6701A", - "C6702G", - "A6704C", - "C6706A", - "G6708C", - "A6710G", - "G6711A", - "A6712G", - "C6717A", - "A6719C", - "G6724A", - "A6727G", - "G6730A", "A6731C", "C6735T", "A6736C", "C6737G", "C6742A", "G6743C", - "C6746G", "A6751G", - "G6752C", "C6753T", "G6757A", "T6759C" ], "G": [ - "K152P" + "T149E", + "T154G" ] }, "labels": { - "aa": "G: K152P" + "aa": "G: T149E, T154G" } }, "children": [ { "name": "NODE_0000153", "node_attrs": { - "div": 0.131, + "div": 0.129, "clade_membership": { "value": "B2" } @@ -22821,6 +22750,8 @@ "G6675A", "C6681A", "C6716T", + "C6746G", + "G6752C", "A6754G", "A6892G", "T7090C", @@ -22842,6 +22773,9 @@ "C13245T" ], "G": [ + "R138S", + "K152P", + "G155A", "T156I" ], "L": [ @@ -22854,27 +22788,27 @@ ] }, "labels": { - "aa": "G: T156I; L: V332A, N1740S; P: P91L, S103P" + "aa": "G: R138S, K152P, G155A, T156I; L: V332A, N1740S; P: P91L, S103P" } }, "children": [ { "name": "KJ627414", "node_attrs": { - "div": 0.131, + "div": 0.129, "accession": "KJ627414", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "B2" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -22900,20 +22834,20 @@ { "name": "KJ627400", "node_attrs": { - "div": 0.131, + "div": 0.129, "accession": "KJ627400", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "B2" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "B2" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -22958,7 +22892,7 @@ { "name": "NODE_0000154", "node_attrs": { - "div": 0.13, + "div": 0.127, "clade_membership": { "value": "B2" } @@ -22994,7 +22928,6 @@ "A12869G" ], "G": [ - "S138R", "I139P", "N140I", "A172T", @@ -23004,26 +22937,849 @@ "T44N" ] }, - "labels": { - "aa": "G: S138R, I139P, N140I, A172T, A229T; P: T44N" - } - }, - "children": [ + "labels": { + "aa": "G: I139P, N140I, A172T, A229T; P: T44N" + } + }, + "children": [ + { + "name": "KJ627397", + "node_attrs": { + "div": 0.134, + "accession": "KJ627397", + "author": { + "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", + "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." + }, + "clade_membership": { + "value": "B2" + }, + "region": { + "value": "South America" + }, + "country": { + "value": "Peru" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A171T", + "A232G", + "T336C", + "T348C", + 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+ "C12848T", + "A12893G" ] } }, "children": [ { - "name": "OP904066", + "name": "PP947580", "node_attrs": { - "div": 0.132, + "div": 0.138, "clade_membership": { "value": "B2" } @@ -23912,150 +24803,216 @@ "branch_attrs": { "mutations": { "nuc": [ - "A972C", - "C1594T", - "C1628T", - "C2719T", - "C2779T", - "A3240G", - "C3712T", - "T3726C", - "T4982C", - "T4985C", - "T5442C", - "T5883C", - "C6071A", - "T6560C", - "C6639T", - "C6777A", - "T6834C", - "A7229T", - "G7979A", - "A8354G", - "T8547A", - "A8756G", - "G9437A", - "T10496C", - "G10658A", - "A10796G", - "A11537G", + "C1140T", + "G1685A", + "A1691G", + "C1868T", + "C3246T", + "C3837A", + "T4386C", + "A5045G", + "A5542G", + "A5940G", + "C6189-", + "C6190-", + "A6191-", + "T6192-", + "A6193-", + "A6194-", + "T6195C", + "-6196C", + "T6201-", + "C6202T", + "C6204T", + "T6205A", + "G6206A", + "A6207T", + "A6208C", + "T6209A", + "-6210C", + "-6211T", + "-6212A", + "-6213A", + "-6214A", + "-6215T", + "T6330C", + "T6441C", + "T6571C", + 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+ "div": 0.138, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A126G", + "A165G", + "T987C", + "T990C", + "T2054A", + "C2206T", + "C2228T", + "A2353T", + "A3070G", + "C3528T", + "A3564G", + "C4230T", + "A4374T", + "T4611C", + "T4635C", + "-4684A", + "G4787A", + "C5322T", + "G5698A", + "C5805T", + "G5871A", + "G5892T", + "-6007T", + "-6008G", + "-6009G", + "G6012T", + "G6014A", + "C6016T", + "T6019C", + "A6020T", + "C6022T", + "T6023A", + "T6024A", + "T6025-", + "A6026-", + "A6027-", + "A6082G", + "C6511T", + "C6513T", + "G6752A", + "G6869A", + "T6945C", + "C7030-", + "T7031-", + "A7033T", + "G7034C", + "-7035A", + "-7036G", + "-7037A", + "C9092T", + "A9877G", + "T10061C", + "C10355A", + "G11687A", + "A12392G", + "T12495C", + "C12716T", + "A12818G" + ], + "F": [ + "I7V" ], "G": [ - "S24G" + "L89F", + "S169N" ], "L": [ - "N954D" + "K904R" + ], + "SH": [ + "D69N", + "M133I", + "-174Y", + "H175Y", + "Y176L", + "L177*", + "*178E", + "E179K", + "K180N", + "N181R", + "R182L", + "L183S" ] }, "labels": { - "aa": "G: S24G; L: N954D" + "aa": "F: I7V; G: L89F, S169N; L: K904R; SH: D69N, M133I, -174Y, H175Y, Y176L, L177*, *178E, E179K, K180N, N181R, R182L, L183S" } } } ] }, { - "name": "NODE_0000163", + "name": "NODE_0000173", "node_attrs": { - "div": 0.133, + "div": 0.134, "clade_membership": { "value": "B2" } @@ -24063,93 +25020,21 @@ "branch_attrs": { "mutations": { "nuc": [ - "G363A", - "A540G", - "C666T", - "A1059G", - "A1511T", - "A1646G", - "C1709T", - "C2428T", - "G2488A", - "T3158A", - "G3519A", - "T4233C", - "G4605A", - "G4778A", - "C5548A", - "G5736A", - "G5764A", - "G5905A", - "C6455A", - "A6470G", - "T6500C", - "G6675A", - "A6736T", - "T6792C", - "A6795G", - "C6816A", - "G6851A", - "A6906C", - "C6997T", - "C7045T", - "C7298T", - "G7314A", - "T7328C", - "C7538T", - "C8930T", - "T10172C", - "T10295C", - "G10307A", - "A10745G", - "A11834G", - "A11879G", - "C11976A", - "T12041C", - "G13034A", - "-13190A" - ], - "F": [ - "L36H" + "C6704T" ], "G": [ - "P70Q", - "K75R", - "L85S", - "T164S", - "-201N", - "S203D", - "D204Q", - "Q205T", - "A226Y", - "Y227N", - "N228A", - "A229D", - "D230T", - "T231S", - "S233L", - "L234S", - "S235-" - ], - "L": [ - "V50I", - "P1604T" - ], - "SH": [ - "L19I", - "V91I", - "A138T" + "P153L" ] }, "labels": { - "aa": "F: L36H; G: P70Q, K75R, L85S, T164S, -201N, S203D, D204Q, Q205T, A226Y, Y227N, N228A, A229D, D230T, T231S, S233L, L234S, S235-; L: V50I, P1604T; SH: L19I, V91I, A138T" + "aa": "G: P153L" } }, "children": [ { - "name": "NODE_0000164", + "name": "NODE_0000174", "node_attrs": { - "div": 0.134, + "div": 0.135, "clade_membership": { "value": "B2" } @@ -24157,74 +25042,41 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1580C", - "C1628T", - "T1733C", - "A4747G", - "C5772T", - "C6396A", - "C6444T", - "-6863C", - "T6864-", - "C6930T", - "A7141G", - "G12593A" + "C1352T", + "A3495G", + "C3528T", + "G4410A", + "G6457T", + "G6694A", + "G9494A", + "T10580C" ], - "M2-1": [ - "K4R" + "G": [ + "A71S", + "E150K" ] }, "labels": { - "aa": "M2-1: K4R" + "aa": "G: A71S, E150K" } }, "children": [ { - "name": "NODE_0000165", + "name": "NODE_0000175", "node_attrs": { - "div": 0.136, + "div": 0.135, "clade_membership": { "value": "B2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A750G", - "G966A", - "-2947A", - "A2949T", - "T2950A", - "A2952T", - "T2954G", - "G2955T", - "T2956C", - "T2958A", - "A2959T", - "T2960A", - "A2961T", - "T2962A", - "A2963-", - "C4107T", - "C4230T", - "T6065C", - "G6244A", - "A6411G", - "T6507C", - "T6624C", - "T6633C", - "T8580C", - "C8936T", - "G9020A", - "A9812G" - ] - } + "mutations": {} }, "children": [ { - "name": "OP904118", + "name": "PP947639", "node_attrs": { - "div": 0.138, + "div": 0.14, "clade_membership": { "value": "B2" } @@ -24232,62 +25084,132 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1020C", - "T1038C", - "T1122C", - "T1186C", - "C1440T", - "A1856T", - "G3315A", - "C3627T", - "T4889C", + "A270T", + "G363A", + "C735T", + "A1302G", + "C1326T", + "T1580C", + "C1677T", + "C1730T", + "C2039T", + "T2943C", + "T2950C", + "T2953C", + "T2958C", + "C3414T", + "A3476G", + "G3714A", + "T4044C", + "G4357A", + "G4575A", + "A5006G", "T5168C", - "A5877G", - "T5965C", - "G6432A", - "C6530T", - "C6621T", + "T5589C", + "A5694G", + "C5772T", + "C6037T", + "A6127G", + "G6142A", + "T6286C", + "C6306T", + "T6494C", + "T6550C", + "A6577T", "C6639T", - "T7268C", - "T8795A", - "A9065T", - "A9170G", - "G9236A", - "T9467C", - "T9491C", - "T9512C", - "A9683G", - "A10039G", - "C10215A", - "T10358C", - "C10518T", - "A10820G", - "A11117G", - "C11297T", - "C11498T" + "T6665C", + "T6704C", + "-6863C", + "T6864-", + "T6965-", + "A6966-", + "T6967-", + "A6968-", + "T6969-", + "A6972T", + "-6975A", + "-6976T", + "-6977A", + "-6978T", + "-6979A", + "-6980A", + "-6981A", + "-6982A", + "-6983T", + "-6984A", + "A6986-", + "G7066T", + "A7067T", + "C7069A", + "T7071C", + "A7076C", + "C7077T", + "T7078A", + "A7080T", + 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@@ "branch_attrs": { "mutations": { "nuc": [ - "C2114T", - "C5836T", - "T6007-", - "G6008-", - "G6009-", - "T6012G", - "A6014G", - "T6016C", - "C6019T", - "T6020A", - "T6022C", - "A6023T", - "A6024T", - "-6025T", - "-6026A", - "-6027A", - "C6174T", - "A11840G", - "C12932T" + "G327A", + "A425G", + "G819A", + "C2653T", + "C4808T", + "C6396A", + "G6875A", + "G10706A", + "A12371T", + "A12821G" ], - "SH": [ - "H115Y", - "Y174-", - "-175H" + "G": [ + "A172E" + ], + "N": [ + "K129R" ] }, "labels": { - "aa": "SH: H115Y, Y174-, -175H" + "aa": "G: A172E; N: K129R" } }, "children": [ { - "name": "OP904137", + "name": "NODE_0000177", "node_attrs": { - "div": 0.137, + "div": 0.139, "clade_membership": { "value": "B2" } @@ -24337,31 +25251,121 @@ "branch_attrs": { "mutations": { "nuc": [ - "G687A", - "T4569G", - "C5400T", - "A6032T", - "A6553T" - ], - "F": [ - "I506M" + "C319T", + "C849T", + "A1298G", + "C1472T", + "G1649A", + "C1676T", + "C2039T", + "C2710T", + "T2933C", + "T2943C", + "T2950C", + 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+ "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T102C", + "G12843A" + ], + "L": [ + "A1893T" + ] + }, + "labels": { + "aa": "L: A1893T" + } + } + } + ] }, { - "name": "NODE_0000167", + "name": "NODE_0000178", "node_attrs": { - "div": 0.138, + "div": 0.14, "clade_membership": { "value": "B2" } @@ -24369,71 +25373,134 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1586A", - "C3233A", - "G5886A", - "G5935A", - "A6545G", - "A7123-", - "G7125A", - "A7126G", - "T7129A", - "A7130T", - "G7132A", - "A7133G", - "G7135A", - "A7136G", - "A7137-", - "G7138-", - "C7139-", - "T7140A", - "G7141A", - "A7142G", - "A7143T", - "-7144T", - "-7145G", - "-7146A", - "-7147A", - "G12896A", - "T13040C" - ], - "F": [ - "T61N" + "T294C", + "C486T", + "T1313C", + "A1331G", + "A1967G", + "A2084G", + "G2677A", + "T3681C", + "T4461C", + "T4635C", + "T4863C", + "T4895C", + "A5069G", + "A5842G", + "T5927C", + "G6121A", + "G6142A", + "A6157G", + "G6450A", + "C6542T", + "G6631A", + "C6635T", 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"nuc": [ + "T150C", + "G3975A", + "T6965A", + "A6971T", + "-6974A", + "-6975A", + "-6976T" + ] + } } }, { - "name": "OP904128", + "name": "OR883669", "node_attrs": { - "div": 0.138, + "div": 0.14, "clade_membership": { "value": "B2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "T192C", + "C6612T", + "-6978T", + "-6979A", + "-6980A", + "-6981A", + "-6982A", + "-6983T", + "-6984A", + "A6986-" + ] + } } } ] @@ -24443,70 +25510,21 @@ ] }, { - "name": "NODE_0000168", + "name": "NODE_0000179", "node_attrs": { - "div": 0.136, + "div": 0.135, "clade_membership": { "value": "B2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A663G", - "A675G", - "T1271C", - "A2458G", - "A2930-", - "T2933G", - "A2934T", - "C2936A", - "T2937C", - "G2938T", - "T2939G", - "C2940T", - "T2942C", - "A2943T", - "T2945A", - "C2946T", - "-2947C", - "T2957C", - "C4611T", - "A6459G", - "G6576A", - "C6860T", - "G6869A", - "T6947C", - "G7019A", - "C7091T", - "G7348A", - "G10397A", - 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"labels": { + "aa": "G: D131N, T168I; P: T80I" + } + } + } + ] }, { - "name": "NODE_0000169", + "name": "NODE_0000181", "node_attrs": { - "div": 0.136, + "div": 0.135, "clade_membership": { "value": "B2" } @@ -24621,24 +25664,19 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6037T", - "T6942A", - "T11039C", - "A11336G" - ], - "SH": [ - "R182W" + "A6106C", + "A6107-", + "C6108-", + "A8429G", + "T10910C" ] - }, - "labels": { - "aa": "SH: R182W" } }, "children": [ { - "name": "OP904016", + "name": "NODE_0000182", "node_attrs": { - "div": 0.138, + "div": 0.136, "clade_membership": { "value": "B2" } @@ -24646,112 +25684,252 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1761G", - "T1826C", - "A3894G", - "C4185T", - "A5764G", - "T5994C", - "C6809T", - "G6835A", - "C7047T", - "C7613T", - "A7686C", - "A7865G", - "A9838C", - "C9962T", - "A10112G", - "G10214A", - "G10481A", - "C10724T", - "A10775G", - "A10881G", - "A12051G" - ], - "G": [ - "T189I", - "S190T", - "A191S", - "R192A", - "S193R", 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{ + "mutations": { + "nuc": [ + "G639A" + ] + } + } + }, + { + "name": "OP904151", + "node_attrs": { + "div": 0.138, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": {} + } + } + ] + }, + { + "name": "NODE_0000193", + "node_attrs": { + "div": 0.138, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ + { + "name": "OP904033", + "node_attrs": { + "div": 0.138, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C1440T", + "C1899T" + ] + } + } + }, + { + "name": "OP904024", + "node_attrs": { + "div": 0.138, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": {} + } + } + ] + } + ] + } + ] } - } + ] } ] } @@ -24855,7 +26442,7 @@ ] }, { - "name": "NODE_0000171", + "name": "NODE_0000194", "node_attrs": { "div": 0.135, "clade_membership": { @@ -24865,68 +26452,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1203T", - 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- "C6886T", - "T6974A", - "T7706C", - "G9305A", - "G9755A" + "C384T", + "T1083C", + "C1358T", + "A1512G", + "C2148T", + "C2785T", + "G3357A", + "C3837T", + "G4473A", + "T4964C", + "T5033C", + "T5081C", + "C5838T", + "C5975A", + "G6456A", + "C6645T", + "C6669A", + "T6741C", + "-6863C", + "C6865-", + "T6884C", + "G6950A", + "A7067C", + "G7068A", + "C7069T", + "A7076T", + "C7077A", + "T7078A", + "A7079T", + "A7080G", + "G7081-", + "G7099A", + "A7105G", + "T8426C", + "C9059T", + "C10520T", + "C10688T", + "C11801T", + "A12134G", + "C12959A", + "A13124T" ], "G": [ - "R192G" - ], - "M": [ - "V23I" + "N141K", + "S235N" ], "P": [ - "L65P" + "T89A" ], "SH": [ - "K160E" + "A161E" ] }, "labels": { - "aa": "G: R192G; M: V23I; P: L65P; SH: K160E" + "aa": "G: N141K, S235N; P: T89A; SH: A161E" } }, "children": [ { - "name": "PP947592", + "name": "PP947637", "node_attrs": { - "div": 0.139, + "div": 0.141, "clade_membership": { "value": "B2" } @@ -25023,51 +26595,25 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1551A", - "A1766G", - "G4786A", - "T5667C", - "C6407T", - "C6605T", - "C6623T", - "A6679G", - "T6969A", - "A6972T", - "-6975C", - "A6985-", - "A6986-", - "C6987-", - "C9847T", - "T10682C", - "A11300G", - "G12221A" - ], - "G": [ - "A54V", - "T120I", - "S126F", - "T144A" - ], - "L": [ - "T894I", - "I1378M" - ], - "M2-1": [ - "R17K" - ], - "P": [ - "V102I" + "C6863T", + "G7034A", + "A12509G", + "A12779G", + "T13194A", + "A13195T", + "C13196A", + "C13197A", + "C13198T", + "G13199C", + "G13200A" ] - }, - "labels": { - "aa": "G: A54V, T120I, S126F, T144A; L: T894I, I1378M; M2-1: R17K; P: V102I" } } }, { - "name": "OM262418", + "name": "NODE_0000197", "node_attrs": { - "div": 0.141, + "div": 0.14, "clade_membership": { "value": "B2" } @@ -25075,71 +26621,54 @@ "branch_attrs": { "mutations": { "nuc": [ - "-24T", - "A25G", - "C26T", - "G28C", - "G29T", - "A30C", - "A32T", - "A33T", - "A34C", - "T35G", - "A37T", - "A38C", - "A39T", - "A327G", - "C996T", - "A1622G", - "G3588A", - 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"labels": { + "aa": "G: T148A, L153P; L: G1745S" + } + } + }, + { + "name": "OP904140", + "node_attrs": { + "div": 0.141, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G981A", + "G1422A", + "T3981C", + "C4029T", + "T5474A", + "-5475T", + "A5861G", + "A5942G", + "A6106C", + "A6107-", + "C6108-", + "A6419C", + "A6445G", + "A6651G", + "A6745G", + "T9374C", + "A10403G", + "T10496C", + "A12088G" + ], + "G": [ + "N58T", + "N67D", + "R138S", + "S139I", + "I140N", + "N141R", + "R142Q", + "Q143T", + "T145Q", + "Q146T", + "T149E", + "E150K", + "K152L", + "L153T", + "T154G", + "G155A", + "A156T", + "T158K", + "K160E", + "E161R", + "R162T", + "T165Q", + "Q166A", + "T168S", + "S169T", + "T170A", + "A172T", + "T173Q", + "Q174T", + "T175P", + "P176N", + "N177T", + "T179N", + "N180Q", + "Q181T", + "T182S", + "S183N", + "N184R", + "R186E", + "E187A", + "S190T", + "A191S", + "R192A", + "S193R", + "R194S", + "N195R", + "G196N", + "A197G", + "T198A", + "Q200T", + "-201Q" + ], + "L": [ + "D1641G" + ], + "P": [ + "A59T" + ], + "SH": [ + "K123R", + "K150R" + ] + }, + "labels": { + "aa": "G: N58T, N67D, R138S, S139I, I140N, N141R, R142Q, Q143T, T145Q, Q146T, T149E, E150K, K152L, L153T, T154G, G155A, A156T, T158K, K160E, E161R, R162T, T165Q, Q166A, T168S, S169T, T170A, A172T, T173Q, Q174T, T175P, P176N, N177T, T179N, N180Q, Q181T, T182S, S183N, N184R, R186E, E187A, S190T, A191S, R192A, S193R, R194S, N195R, G196N, A197G, T198A, Q200T, -201Q; L: D1641G; P: A59T; SH: K123R, K150R" + } + } + } + ] } ] } @@ -25513,9 +27211,9 @@ ] }, { - "name": "NODE_0000177", + "name": "NODE_0000203", "node_attrs": { - "div": 0.137, + "div": 0.135, "clade_membership": { "value": "B2" } @@ -25523,44 +27221,35 @@ "branch_attrs": { "mutations": { "nuc": [ - "G369A", - "C1358T", - "T2942G", - "G3579A", - "T4434C", - "A5764G", - "A6538G", - "T6747C", - "A6846G", - "T6855C", - "C6879A", - "C7432T", - "T9671C", - "T9735C", - "T10550C", - "G10658A", - "A11219G", - "A12110T" + "A1470G", + "C2617T", + "G5616A", + "G6637A", + "-6863A", + "T6864-", + "T6947C", + "T7073C", + "A9281G", + "C9617T", + "A12998G" ], "G": [ - "T98A" - ], - "L": [ - "T89I" + "D131N", + "L234P" ], - "SH": [ - "I91V" + "P": [ + "S75G" ] }, "labels": { - "aa": "G: T98A; L: T89I; SH: I91V" + "aa": "G: D131N, L234P; P: S75G" } }, "children": [ { - "name": "OP904141", + "name": "OP904034", "node_attrs": { - "div": 0.139, + "div": 0.137, "clade_membership": { "value": "B2" } @@ -25568,70 +27257,51 @@ "branch_attrs": { "mutations": { "nuc": [ - "G640A", - "G1426A", - "A1887G", - "A1963G", - "T1982C", - "T2024C", - "G3024A", - "C3735T", - "G4042A", - "C4272T", - "T4404C", - "A4835G", - "T6139C", - "G6430T", - "T6507C", - "T6584C", - "-6863C", - "T6864-", - "T6925C", - "A6933G", - "T6942C", - "T6947C", - "T7096A", - "A7321G", - "T7607C", - "T7638C", - "C8249T", - "C9617T", - "C10045T", - "G11687A", - "C11810T", - "C12455T" - ], - "F": [ - "D331N" - ], - "G": [ - "V62L", - "L113P", - 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"branch_attrs": { - "mutations": {} - }, "children": [ { - "name": "NODE_0000182", + "name": "PP947683", + "node_attrs": { + "div": 0.14, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T10959C" + ] + } + } + }, + { + "name": "NODE_0000208", "node_attrs": { "div": 0.141, "clade_membership": { @@ -25877,11 +27510,33 @@ } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "A762G", + "C1104T", + "G1850A", + "C4625T", + "G6797A", + "T9630C" + ], + "F": [ + "P525L" + ], + "G": [ + "S183R", + "N184K", + "R185E", + "R186A", + "E187T" + ] + }, + "labels": { + "aa": "F: P525L; G: S183R, N184K, R185E, R186A, E187T" + } }, "children": [ { - "name": "PP947682", + "name": "PP947603", "node_attrs": { "div": 0.141, "clade_membership": { @@ -25891,20 +27546,20 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1441C", - "C4029T" + "T6549C", + "G12070A" ], - "P": [ - "L65P" + "L": [ + "S1635N" ] }, "labels": { - "aa": "P: L65P" + "aa": 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], - "L": [ - "I1104T", - "V1107A" + "P": [ + "E236K" ] }, "labels": { - "aa": "G: L136P, T156A, T189K, S190T, A191S, S193R, R194S, N195R, G196N, A197G, T198A; L: I1104T, V1107A" + "aa": "P: E236K" } }, "children": [ { - "name": "OP904105", + "name": "OP904119", "node_attrs": { - "div": 0.132, + "div": 0.139, "clade_membership": { "value": "B2" } @@ -26156,21 +29343,327 @@ } }, { - "name": "OP904036", + "name": "MW221992", "node_attrs": { - "div": 0.132, + "div": 0.139, + "accession": "MW221992", + "author": { + "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", + "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." + }, "clade_membership": { "value": "B2" + }, + "region": { + "value": "Oceania" + }, + "country": { + "value": "Australia" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "C6106A", + "-6107A", + "-6108C", + "C6997-", + "A6998C", + "C7004A", + "T7005A", + "A7006C", + "G7007T", + "-7009G", + "-7010A", + 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"T12341C", - "G12626A", - "A12689G", - "T13037C" - ], - "G": [ - "L85P" - ], - "L": [ - "D546N" - ] - }, - "labels": { - "aa": "G: L85P; L: D546N" - } - } - } - ] - }, - { - "name": "NODE_0000220", - "node_attrs": { - "div": 0.129, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A6087G", - "T6500C", - "G6711A" - ] - } - }, - "children": [ - { - "name": "OP904042", - "node_attrs": { - "div": 0.131, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G2377A", - "C3038T", - "G4617A", - "A5368G", - "A6054T", - "G6144A", - "G6471A", - "T6499C", - "G6708A", - "G6709A", - "A6710C", - "G6882A", - "C6941T", - "G7034A", - "C7537T", - "G8708A", - "G8802A", - "A8927C", - "C9185T", - "A9662G", - "A9794G", - "G10463A", - "G10592A", - "T12083C", - "G12399A", - "G12626A", - "T13037C" - ], - "G": [ - "L85P", - "S232F" - ], - "L": [ - "T124I", - "D546N", - "G1745S" - ], - "M2-2": [ - "T41A" - ] - }, - "labels": { - "aa": "G: L85P, S232F; L: T124I, D546N, G1745S; M2-2: T41A" - } - } }, { - "name": "NODE_0000221", + "name": "NODE_0000251", "node_attrs": { - "div": 0.133, + "div": 0.13, "clade_membership": { "value": "B2" } @@ -29888,103 +31284,18 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1982C", - "G4212A", - "G5706A", - "T6007-", - "G6008-", - "G6009-", - "T6012G", - "A6014G", - "T6016C", - "C6019T", - "T6020A", - "T6022C", - "A6023T", - "A6024T", - "-6025T", - "-6026A", - "-6027A", - "C6035A", - "A6054G", - "C6477T", - "T6535C", - "T6558C", - "T6560C", - "T6612C", - "T6633C", - "A6672G", - "C6691A", - "A6692C", - "G6693A", - "A6694G", - "G6695A", - "A6696G", - "G6701A", - "C6702G", - "A6704T", - "C6706A", - "G6708C", - "A6710G", - "A6712G", - "C6717A", - "A6719C", - "A6720C", - "G6724A", - "A6727G", - "G6730A", - "A6731G", - "G7070A", - "A7104G", - "C7637A", - "T9602C", - "C9653T", - "C11826T", - "A12179G", - "G12893A", - "-13190A" - ], - "G": [ - "L85S", - "L105P", - "S138R", - "I139S", - "N140I", - "R141N", - "Q142R", - "T143Q", - "Q145T", - "T146Q", - "E149T", - "K150E", - "T153L", - "G154T", - "T155G", - "T156A", - "K158T", - "E160K", - "K161E", - "E162R", - "Q207-", - "T220L", - "E221K", - "K222S" - ], - "SH": [ - "Y174-", - "-175H", - "T181N" + "C6747T", + "T13189-", + "A13190-", + "-13206T" ] - }, - "labels": { - "aa": "G: L85S, L105P, S138R, I139S, N140I, R141N, Q142R, T143Q, Q145T, T146Q, E149T, K150E, T153L, G154T, T155G, T156A, K158T, E160K, K161E, E162R, Q207-, T220L, E221K, K222S; SH: Y174-, -175H, T181N" } }, "children": [ { - "name": "NODE_0000222", + "name": "NODE_0000252", "node_attrs": { - "div": 0.133, + "div": 0.13, "clade_membership": { "value": "B2" } @@ -29992,15 +31303,17 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6747T" + "G8852A", + "C9653T", + "A10592G" ] } }, "children": [ { - "name": "MZ504966", + "name": "OP904066", "node_attrs": { - "div": 0.136, + "div": 0.132, "clade_membership": { "value": "B2" } @@ -30008,113 +31321,57 @@ "branch_attrs": { "mutations": { "nuc": [ - "C20T", - "A21C", - "-24A", - "A34T", - "T35-", - "A36-", - "T178C", - "T864C", - "G1077A", - "C1658A", - "T2144-", - "A2145-", - "T2957C", - "T2958C", - "T2982C", - "T2983C", - "T2989C", - "A3150G", - "T4434C", - "C5772T", - "T5929C", - "G5969A", - "C5989A", - "T6023C", - "G6054A", - "C6106A", - "-6107A", - "-6108C", - "C6539T", - "A6646G", - "T6965-", - "A6966-", - "T6967-", - "A6968-", - "T6969-", - "A6970-", - "A6971-", - "A6972-", - "-6975A", - "-6976T", - "-6977A", - "-6978T", - "-6979A", - "-6980A", - "-6981A", - "-6982A", - "-6983T", - "-6984A", - "A6986-", - "T7544C", - "C8564T", - "T8915G", - "A9431G", - "T10008C", - "G10958A", - "A10961G", - "C11297T", - "T11949C", - "T12746C", - "A13088T", - "C13196A", - "G13247A", - "-13283T", - "-13284A", - "-13285G", - "-13286T", - "-13287A", - "-13288A", - "-13289C", - "G13292A", - "A13294G", - "C13296T", - "T13297A", - "-13300A", - "-13301A", - "-13302A", - "-13303T", - "-13304A", - "-13305C", - "-13306G", - "-13307A", - "-13308C", - "-13309T", - "-13310T", - "-13311A", - "-13312C", - "-13313T" + "A972C", + "C1358T", + "C1594T", + "C1628T", + "C2719T", + "C2779T", + "A3240G", + "C3712T", + "T3726C", + "T4982C", + "T4985C", + "T5442C", + "T5883C", + "C6071A", + "T6560C", + "C6639T", + "C6777A", + "T6834C", + "A7229T", + "G7979A", + "A8354G", + "T8547A", + "A8756G", + "G9437A", + "T10496C", + "G10658A", + "A10796G", + "A11537G", + "C11724T", + "G12368A" ], "G": [ - "T98I", - "T134A" + "L105P", + "A172V" ], - "SH": [ - "R159K", - "L166I", - "L177P" + "L": [ + "S461T" + ], + "P": [ + "S116L" ] }, "labels": { - "aa": "G: T98I, T134A; SH: R159K, L166I, L177P" + "aa": "G: L105P, A172V; L: S461T; P: S116L" } } }, { - "name": "NODE_0000223", + "name": "NODE_0000253", "node_attrs": { - "div": 0.133, + "div": 0.131, "clade_membership": { "value": "B2" } @@ -30122,15 +31379,24 @@ "branch_attrs": { "mutations": { "nuc": [ - "A7067T" + "A1484G", + "G2554A", + "T3531C", + "A4754G", + "-7009A", + "-7010A", + "-7015A", + "A8501G", + "G8711A", + "T12545C" ] } }, "children": [ { - "name": "OP904117", + "name": "OP904111", "node_attrs": { - "div": 0.142, + "div": 0.136, "clade_membership": { "value": "B2" } @@ -30138,63 +31404,28 @@ "branch_attrs": { "mutations": { "nuc": [ - "C486T", - "C577T", - "C699T", - "T990C", - "T1038C", - "A1116G", - "T1212C", - "C1519T", - "C1658T", - "A2080G", - "C2246T", - "T2383C", - "T2942C", - "G3013T", - "A3022G", - "G3024A", - "C3186T", - "C3192A", - "A3318G", - "C3390T", - "C3414A", - "G3516A", - "C3544T", - "G3579A", - "C3585T", - "C3624A", - "C3792T", - "T3882C", - "G4239A", - "T4656C", - "T5018C", - "T5024C", - "G5087A", - "T5265G", - "G5364A", - "G5411A", - "C5805T", - "G5905A", - "T5988C", - "A6060G", - "T6140C", - "T6384C", - "T6413C", - "G6432A", - "C6444T", - "C6602T", - "A6619T", - "T6792C", - "A6881G", - "T6965C", - "-7009A", - "-7010A", + "T207C", + "T390C", + "T1017C", + "C1140T", + "A1302G", + "C1806T", + "C1940T", + "T2021C", + "T2404C", + "C2860T", + "A2935G", + "C3567T", + "A3648G", + "G4353A", + "T5503C", + "C6816T", + "G6853A", + "C6886T", "-7011A", "-7012G", "-7013T", "-7014T", - "-7015A", "A7017T", "A7018T", "G7019T", @@ -30203,7 +31434,6 @@ "A7023C", "T7025C", "T7026A", - "A7028G", "C7030A", "T7031A", "C7032A", @@ -30211,7 +31441,6 @@ "-7035C", "-7036A", "-7037C", - "A7041C", "A7043C", "C7044T", "C7045A", @@ -30219,89 +31448,59 @@ "C7047A", "A7048T", "A7049G", - "C7051A", - "A7052T", - "C7053T", - "T7054G", - "A7055T", - "A7057T", - "G7059A", + "C7051-", + "A7052-", + "C7053-", + "T7054-", + "A7055-", + "T7056-", + "G7059T", "A7060G", "A7061T", - "T7062G", - "G7064A", - "G7066A", - "G7068A", - "A7070T", - "T7071A", - "A7074-", - "T7075-", - "A7076-", - "C7077-", - "T7078-", - "A7079-", - "A7080-", - "C7151T", - "G8048A", - "C8729T", - "T8750C", - "C9251T", - "T9390C", - "C9401T", - "C9743T", - "G9746A", - "G10154A", - "C10244T", - "C10280T", - "A10469G", - "C10526A", - "C10724T", - "T10781C", - "C11159T", - "C11180T", - "A11636G", - "C11810T", - "G11825A", - "A12249G", - "A12257G", - "A12554G", - "A12557G", - "A12566G", - "A12659C", - "C12776T", - "C12959T" + "T7065A", + "A7067C", + "C7069T", + "G7070A", + "T7075C", + "A7076T", + "C7077A", + "T7078A", + "A7079T", + "A7080G", + "G7081-", + "G7125A", + "A7321G", + "C8033T", + "T8603C", + "G8612A", + "A8744G", + "G9497A", + "G10272T", + "A11270G", + "G12062A", + "A13101G" ], "G": [ - "L56S", - "P119L", - "I125F" + "D204N" ], "L": [ - "I1695V" - ], - "M2-1": [ - "L177V" - ], - "M2-2": [ - "S55N" + "N52S", + "A1036S", + "I1979V" ], "P": [ - "P91L", - "K278R" - ], - "SH": [ - "A138T" + "I19V" ] }, "labels": { - "aa": "G: L56S, P119L, I125F; L: I1695V; M2-1: L177V; M2-2: S55N; P: P91L, K278R; SH: A138T" + "aa": "G: D204N; L: N52S, A1036S, I1979V; P: I19V" } } }, { - "name": "NODE_0000224", + "name": "MK588637", "node_attrs": { - "div": 0.135, + "div": 0.133, "clade_membership": { "value": "B2" } @@ -30309,83 +31508,89 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1350G", - "C1677T", - "A1835T", - "C2039T", - "T2818A", - "A2977T", - "T2978G", - "G2979A", - "A2980G", - "G2981C", - "C3038T", - "T3706C", - "T4889C", - "A6964G", - "A7050C", - "G7066T", - "C7069A", - "T7071C", - "A7076C", - "C7077T", - "T7078A", - "A7080T", - "T7544C", - "C9660T", - "G9920A", - "G10498A", - "T11134C", - "C12014T", - "T12677C" + "A51G", + "T843C", + "C1358T", + "A2000G", + "C4817T", + "C6106A", + "-6107A", + "-6108C", + "A6316G", + "-6975A", + "-6976A", + "-6977C", + "-6978G", + "-6979A", + "-6980T", + "-6981G", + "-6982A", + "-6983A", + "-6984A", + "A6986C", + "C6988A", + "T6990-", + "G6991-", + "A6992-", + "A6993-", + "A6994-", + "A6995-", + "C6996-", + "C6997-", + "A6998-", + "A6999-", + "A7000-", + "A7001-", + "A7002-", + "A7003-", + "C7004-", + "T7005-", + "A7006-", + "G7007-", + "-7011C", + "-7012T", + "-7013A", + "-7014G", + "A7688G", + "A7760T", + "A10026G", + "T10187C", + "C10526T", + "G11768A", + "C13103T", + "-13188G", + "-13189C", + "A13194T", + "T13195A", + "A13197C", + "T13198C", + "A13200G", + "-13204C", + "-13205T", + "-13207T", + "-13208G", + "G13209A" ], - "L": [ - "S1111N", - "V1323A" + "G": [ + "S24G" ], - "P": [ - "T35A" + "L": [ + "N954D" ] }, "labels": { - "aa": "L: S1111N, V1323A; P: T35A" - } - }, - "children": [ - { - "name": "OP904110", - "node_attrs": { - "div": 0.135, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "OP904057", - "node_attrs": { - "div": 0.135, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": {} - } + "aa": "G: S24G; L: N954D" } - ] + } } ] } ] }, { - "name": "NODE_0000225", + "name": "NODE_0000254", "node_attrs": { - "div": 0.133, + "div": 0.13, "clade_membership": { "value": "B2" } @@ -30393,84 +31598,31 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1158T" + "A13191-", + "C13196A", + "G13199C", + "-13207C", + "-13208A" ] } }, "children": [ { - "name": "NODE_0000226", + "name": "NODE_0000255", "node_attrs": { - "div": 0.136, + "div": 0.13, "clade_membership": { "value": "B2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A219G", - "A339G", - "G489A", - "C1191T", - "A1268G", - "C1504T", - "T2024C", - "G2042A", - "A2081G", - "C2428T", - "G2581A", - "G2845A", - "G3081A", - "G3453A", - "T3945C", - "C4185T", - "G4542A", - "C4611T", - "T4955C", - "T5033C", - "G5670A", - "C5836A", - "T6068C", - "T6146C", - "T6549C", - "C6655T", - "G6694A", - "G6817A", - "A6964G", - "G7700A", - "G8708A", - "T8817C", - "G8891A", - "C9533A", - "G9596A", - "A9650T", - "G10130A", - "T10211C", - "C10238T", - "T10838C", - "G12617A" - ], - "G": [ - "E150K", - "A191T" - ], - "P": [ - "T86I" - ], - "SH": [ - "H115N" - ] - }, - "labels": { - "aa": "G: E150K, A191T; P: T86I; SH: H115N" - } + "mutations": {} }, "children": [ { - "name": "OP904026", + "name": "NODE_0000256", "node_attrs": { - "div": 0.139, + "div": 0.132, "clade_membership": { "value": "B2" } @@ -30478,59 +31630,284 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1988T", - "A3756G", - "C3954T", - "T4083C", - "T4191C", - "T4215C", - "C4272T", - "G5072A", - "A5129G", - "T5541C", - "A5861G", - "T6477A", - "C6557T", - "C6639T", - "T6759C", - "C6771T", - "T7021C", - "T7241C", - "T7610C", - "A7652G", - "C7944T", - "C7988T", - "C7994T", - "A8162G", - "C8564T", - "T8969C", - "A10820G", - "T10877A", - "C10946T", - "T11000C", - "G11093A", - "C11516T", - "A11735G", - "C11877T", - "C12455T", - "G12593A" + "G1471A", + "A1811G", + "T1832C", + "A2970C", + "G3013A", + "C3426T", + "T4041C", + "G4617A", + "T5751C", + "G5886A", + "C5904T", + "A6219G", + "G6525A", + "T6792A", + "A6805G", + "A6916-", + "A6917-", + "C6918A", + "-6919G", + "-6920C", + "T8165A", + "A9794G", + "C11841T", + "T11882C", + "T12017C", + "C13058T" ], "G": [ - "S104F" + "N184K", + "T188A", + "T189A", + "-225A" ], - "SH": [ - "K123R" + "L": [ + "P1559S" + ], + "P": [ + "S75N" ] }, "labels": { - "aa": "G: S104F; SH: K123R" + "aa": "G: N184K, T188A, T189A, -225A; L: P1559S; P: S75N" } - } + }, + "children": [ + { + "name": "OP904067", + "node_attrs": { + "div": 0.135, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C546T", + "C883T", + "T909C", + "T1005C", + "C1718T", + "A2296T", + "C2671T", + "C3363T", + "C3639T", + "C5716T", + "G5871A", + "C5906T", + "A5963G", + "T5965C", + "G6121A", + "G7064C", + "G7070A", + "A7074C", + "T7075A", + "A7076C", + "C7077T", + "T7078A", + "A7080T", + "T7505C", + "G8191A", + "A8209G", + "C8646T", + "C8936T", + "G9272A", + "T9923C", + "A10118G", + "G10706A", + "A11255G", + "T11330C", + "C11976T", + "T11981C", + "G12209A" + ], + "L": [ + "S342N", + "N348S", + "P494S", + "P1604S" + ], + "SH": [ + "A138V", + "K157R", + "Y158H" + ] + }, + "labels": { + "aa": "L: S342N, N348S, P494S, P1604S; SH: A138V, K157R, Y158H" + } + } + }, + { + "name": "MH828685", + "node_attrs": { + "div": 0.137, 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D947S, L948P, L949S, L950V; M: K193N; N: L47S, Y69S, C71R, S88T, K102N, D115E, L138S, D156H, I160M, T175S, R197S, G274E, T286P, K309T, A316P, G340R, F348L; SH: N25K, I85S, T116M, -175Y, Y176L, L177*, *178E, E179K, K180N, T181R, R182L, L183S" + } + } + } + ] }, { - "name": "NODE_0000227", + "name": "NODE_0000257", "node_attrs": { - "div": 0.136, + "div": 0.131, "clade_membership": { "value": "B2" } @@ -30538,172 +31915,115 @@ "branch_attrs": { "mutations": { "nuc": [ - "T636C", - "C2003T", - "C2752T", - "G3321A", - "T8054C", - "A8978G" + "G3612A", + "G3828A", + "T5018C", + "A6410G", + "T6741C", + "C7709T" + ], + "G": [ + "K55R", + "R192A", + "Q200T", + "-201Q" ] + }, + "labels": { + "aa": "G: K55R, R192A, Q200T, -201Q" } }, "children": [ { - "name": "NODE_0000228", + "name": "NODE_0000258", "node_attrs": { - "div": 0.138, + "div": 0.133, "clade_membership": { "value": "B2" } }, "branch_attrs": { "mutations": { - "nuc": [ - "C1478T", - "C1628T", - "C3730T", - "T4389C", - "T4521C", - 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A197G, T198A; L: I1104T, V1107A" } }, "children": [ { - "name": "OP904009", + "name": "OP904105", "node_attrs": { - "div": 0.139, + "div": 0.133, "clade_membership": { "value": "B2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "G4604A", - "G6931A", - "T10513C", - "T10514C" - ], - "F": [ - "R518K" - ], - "G": [ - "-201N", - "N202S", - "S203D", - "D204Q", - "Q205T", - "A226Y", - "Y227N", - "N228T", - "A229D", - "D230T", - "T231S", - "S232P", - "P233L", - "L234S", - "S235-" - ], - "L": [ - "I1116T" - ] - }, - "labels": { - "aa": "F: R518K; G: -201N, N202S, S203D, D204Q, Q205T, A226Y, Y227N, N228T, A229D, D230T, T231S, S232P, P233L, L234S, S235-; L: I1116T" - } + "mutations": {} } }, { - "name": "NODE_0000229", + "name": "OP904036", "node_attrs": { - "div": 0.139, + "div": 0.133, "clade_membership": { "value": "B2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T2215C", - "T4836C", - "A5006T" - ], - "M2-1": [ - "Y34H" - ] - }, - "labels": { - "aa": "M2-1: Y34H" - } - }, - "children": [ - { - "name": "OP904020", - "node_attrs": { - "div": 0.139, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "OP904018", - "node_attrs": { - "div": 0.139, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + "mutations": {} + } } ] }, { - "name": "NODE_0000230", + "name": "NODE_0000259", "node_attrs": { "div": 0.136, "clade_membership": { @@ -30713,15 +32033,136 @@ "branch_attrs": { "mutations": { "nuc": [ - "G5673A" + "A513G", + "A555G", + "A945G", + "T1186C", + "A1367G", + "T1469C", + "A1475G", + "A1531G", + "G1550A", + "T1559C", + "A2000G", + "T2275C", + "G2446A", + "C2494T", + "T2956C", + "T2957C", + "G3321A", + "T3486C", + "T3573C", + "T3576C", + "G3615A", + "T4050C", + "C4419T", + "G5009A", + "A5634G", + "G5790A", + "T5826C", + "C5904T", + "G5914A", + "A6003G", + "T6458C", + "C6608A", + "A6688G", + "A6694C", + "G6708A", + "G6709A", + "G6711A", + "C6713A", + 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T175A, L176A, N177T, T178Q, N180L, Q181N, S183T, R185Q, R186T, E187S, T188N, T189R, S190R, A191E, S193T, R194T, N195T, G196S, T198R, S213P, T219Y, T223H, -224N, L234P; L: I496T, K756R, I962V, P1559S; P: E95G; SH: E141K" } }, "children": [ { - "name": "OP904177", + "name": "OP904144", "node_attrs": { - "div": 0.138, + "div": 0.14, "clade_membership": { "value": "B2" } @@ -30729,46 +32170,83 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1551A", - "C2494T", - "C2940T", - "T4284C", - "G4626A", - "A4993G", - "T5796C", - "T5881C", - "C6632A", + "G255A", + "G459A", + "G3579A", + "G3807A", + "C4029T", + "T4158C", + "T4233C", + "T4545C", + "G4605A", + "C4610T", + "T4988C", + "T5225C", + "T5475C", + "C5724T", + "C6071T", + "T6178G", + "T6489C", + "T6499C", + "C6570T", + "T6633C", "T6653C", - "C9107T", - "T10479C", - "T10496C", - "C10520T", - "A10595G", - "G11582A" - ], - "G": [ - "A129D", - "L136P" + "T6656C", + "A6658G", + "C6689T", + "C6691A", + "G6693C", + "A6698G", + "A6699C", + "C6703A", 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"G11066A", + "A12899G" ], "G": [ - "A123T", - "N180D", - "D204N", - "L234P" + "E63G", + "S138R", + "I139S", + "N140I", + "R141N", + "Q142R", + "T143Q", + "Q145T", + "T146Q", + "A147T" ], - "L": [ - "R174K" + "M": [ + "G246R" ], "P": [ - "S74N" - ], - "SH": [ - "S151P" + "G31A" ] }, "labels": { - "aa": "G: A123T, N180D, D204N, L234P; L: R174K; P: S74N; SH: S151P" + "aa": "G: E63G, S138R, I139S, N140I, R141N, Q142R, T143Q, Q145T, T146Q, A147T; M: G246R; P: G31A" } } }, { - "name": "NODE_0000232", + "name": "OP904154", "node_attrs": { - "div": 0.141, + "div": 0.142, "clade_membership": { "value": "B2" } @@ -30876,155 +32416,62 @@ "branch_attrs": { "mutations": { "nuc": [ - "T357C", - "T450C", - "T1817C", - "T1826C", - "C2242T", - "G2300A", - "T2788C", - "T3068C", - "A3174G", - "G3489A", - "G3588A", - "C4128T", - "G4416A", - "A4509G", - "A5237G", - "A5343T", - "T5471A", - "A5472T", - "T5475A", - "A5517G", - "A5742T", - "A5833G", - "T5965C", - "C6143T", - "C6188-", + "T2452A", + "T3031C", + 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"clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G363A", - "A1495G", - "A3645G", - "G5969A", - "T6704C", - "T6792C", - "T6843C", - "T6893C" - ], - "G": [ - "L153P" - ], - "P": [ - "K83R" - ], - "SH": [ - "R159K" - ] - }, - "labels": { - "aa": "G: L153P; P: K83R; SH: R159K" - } - } - }, - { - "name": "OR883664", - "node_attrs": { - "div": 0.142, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C2915T", - "A5355G", - "C5951T", - "C6938A", - "G10020A", - "T10868C", - "A12476G" - ], - "G": [ - "T231K" - ], - "L": [ - "V952I" - ], - "SH": [ - "T153I" - ] - }, - "labels": { - "aa": "G: T231K; L: V952I; SH: T153I" - } - } + "aa": "G: L105P" } - ] + } } ] } @@ -31035,9 +32482,9 @@ ] }, { - "name": "NODE_0000233", + "name": "NODE_0000261", "node_attrs": { - "div": 0.136, + "div": 0.13, "clade_membership": { "value": "B2" } @@ -31045,69 +32492,16 @@ "branch_attrs": { "mutations": { "nuc": [ - "A570G", - "A1811C", - "A2930-", - "A2934T", - "C2936A", - "T2937C", - "G2938T", - "T2939G", - "C2940T", - "T2942C", - "A2943T", - "T2945A", - "C2946T", - "-2947C", - "A3035G", - "C3294T", - "C3474A", - "G4626A", - "T5415C", - "G5601A", - "T6624C", - "T6653C", - "T6704C", - "T6767C", - "A6903T", - "C7742T", - "C7851T", - "A8351G", - "A9110G", - "G9716A", - "G9755A", - "A9848T", - "G10025A", - "G10634A", - "T11249A", - "C11535T", - "A13194T", - "T13195A", - "A13197C", - "T13198C", - "C13199G", - "A13200G", - "-13204C", - "-13205T", - "C13207T", - "A13208G", - "G13209A" - ], - "G": [ - "L136P", - "L153P", - "L176P" + "G5736A", + "A10592G" ] - }, - "labels": { - "aa": "G: L136P, L153P, L176P" } }, "children": [ { - "name": "OP904017", + "name": "NODE_0000262", "node_attrs": { - "div": 0.14, + "div": 0.131, "clade_membership": { "value": "B2" } @@ -31115,132 +32509,27 @@ "branch_attrs": { "mutations": { "nuc": [ - "G687A", - "C996T", - "A1107G", - "A1514G", - "C1724T", - "T1820A", - "G1928A", - "C2039T", - "C2896T", - "G2939A", - "T2968A", - "A3171G", - "A3384G", - "T3762C", - "C4174T", - "T4284C", - "T4521C", - "G4617T", - "G4787A", - "A5219G", - "C5316T", - "A5470T", - "T5471A", - "A5479G", - "A5559G", - "C5904T", - "T6101C", - "C6513T", - "C6643T", - "A6714T", - "G6731A", - "A6762G", - "C6912T", - "T6969-", - "A6970-", - "A6971-", - "A6972-", - "A6973-", - "T6974-", - "-6978T", - "-6979A", - "-6980A", - "-6981A", - "-6982A", - "-6983T", - "-6984A", - "C6988-", - "T7283C", - "T7430C", - "C7448T", - "A7649G", - "A8723G", - "G9335A", - "T9404C", + "A3933G", + "A6003G", + "T6195C", + "T6507C", + "T6747C", "G9581A", - "C9761T", - "T9770C", - "A10019G", - "A10512G", - "C10520T", - "G10808A", - "A10976G", - "A11681G", - "A11873G", - "A12893G", - "A12929G" - ], - "G": [ - "H133Y", - "R162K" + "G10614A" ], "L": [ - "I1116V" - ], - "SH": [ - "I22M" - ] - }, - "labels": { - "aa": "G: H133Y, R162K; L: I1116V; SH: I22M" - } - } - }, - { - "name": "NODE_0000234", - "node_attrs": { - "div": 0.137, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C5782T", - "G5969A", - "C6106A", - "-6108C", - "T6391C", - "T6458C", - "G6546A", - "T6656C", - "G6743A", - "G7700A", - "C11096T", - "T11252C", - "A12236G" - ], - "G": [ - "V71A", - "L137P", - "R166Q" - ], - "SH": [ - "R159K" + "V1150I" ] }, "labels": { - "aa": "G: V71A, L137P, R166Q; SH: R159K" + "aa": "L: V1150I" } }, "children": [ { - "name": "PP947561", + "name": "OP904060", "node_attrs": { - "div": 0.141, + "div": 0.132, "clade_membership": { "value": "B2" } @@ -31248,102 +32537,239 @@ "branch_attrs": { "mutations": { "nuc": [ - "A126G", - "A165G", - "A579G", - "T987C", - "T990C", - "T2054A", - "C2206T", - "C2228T", - "A2353T", - "A3070G", - "C3528T", - "A3564G", - "C4230T", - "A4374T", - "T4635C", - "-4684A", - "G4787A", - "C5322T", - "G5698A", - "C5805T", - "G5871A", - "G5892T", - "-6007T", - "-6008G", - "-6009G", - "G6012T", - "G6014A", - "C6016T", - "T6019C", - "A6020T", - "C6022T", - "T6023A", - "T6024A", - "T6025-", - "A6026-", - "A6027-", - "A6082G", - "-6107A", - "C6511T", - "C6513T", - "G6752A", - "G6869A", - "T6945C", - "C7030-", - "T7031-", - "A7033T", - "G7034C", - "-7035A", - "-7036G", - "-7037A", - "C9092T", - "A9877G", - "T10061C", - "C10355A", - "G11687A", - "A12392G", - "T12495C", - "C12716T", - "A12818G", - "C12848T", - "A12893G" + "G189A", + "T766C", + "G873A", + "C2634A", + "A2980G", + "C3159T", + "A3171G", + "G3579A", + "G3729A", + "T3741C", + "T4053C", + "C4206T", + "A5536G", + "G5943A", + "C6077A", + "G6142A", + "A6410G", + "A6470G", + "T6893C", + "A7688G", + "C8895T" ], - "F": [ - "I7V" + "G": [ + "K55R", + "K75R" + ], + "M": [ + "P157H" + ], + "SH": [ + "T15A" + ] + }, + "labels": { + "aa": "G: K55R, K75R; M: P157H; SH: T15A" + } + } + }, + { + "name": "MZ504964", + "node_attrs": { + "div": 0.134, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A18T", + "A19C", + "C20A", + "-24A", + "A25C", + "A34-", + "A1304G", + "A1448G", + "A1605G", + "A1643G", + "C2810T", + "A3032G", + "G3081A", + "A3888T", + "A4131G", + "T4386C", + "C4476T", + "T4554A", + "G5364A", + "A6063G", + "C6106A", + "-6107A", + "-6108C", + "G6493A", + "C6666T", + "T6759C", + "C8117T", + "C8552T", + "G8612A", + "A8662G", + "T8768C", + "A9074G", + "T9095C", + "T9156C", + "C9761T", + "G9827A", + "G10093A", + "T10766C", + "C11114T", + "C11513T", + "C12605T", + "T12755C", + "T13032C", + "-13283T", + "-13284A", + "-13285G", + "-13286T", + "-13287A", + "-13288A", + "-13289C", + "G13292A", + "A13294G", + "C13296T", + "T13297A", + "-13300A", + "-13301A", + "-13302A", + "-13303T", + "-13304A", + "-13305G", + "-13306A", + "-13307A", + "-13308C", + "-13309T", + "-13310A" ], "G": [ - "L89F", - "S169N" + "V83I" ], "L": [ - "K904R" + "N499S", + "R976H" ], - "SH": [ - "D69N", - "M133I", - "-174Y", - "H175Y", - "Y176L", - "L177*", - "*178E", - "E179K", - "K180N", - "N181R", - "R182L", - "L183S" + "P": [ + "I19M", + "I120V" ] }, "labels": { - "aa": "F: I7V; G: L89F, S169N; L: K904R; SH: D69N, M133I, -174Y, H175Y, Y176L, L177*, *178E, E179K, K180N, N181R, R182L, L183S" + "aa": "G: V83I; L: N499S, R976H; P: I19M, I120V" } } + } + ] + }, + { + "name": "NODE_0000263", + "node_attrs": { + "div": 0.134, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G363A", + "A540G", + "C666T", + "A1059G", + "A1511T", + "A1646G", + "C1709T", + "C2428T", + "G2488A", + "T3158A", + "G3519A", + "T4233C", + "G4605A", + "G4778A", + "C5548A", + "G5764A", + "G5905A", + "C6455A", + "A6470G", + "T6500C", + "G6675A", + "A6736T", + "T6792C", + "A6795G", + "C6816A", + "G6851A", + "A6906C", + "C6997T", + "C7045T", + "C7298T", + "G7314A", + "T7328C", + "C7538T", + "C8930T", + "C9653T", + "T10172C", + "T10295C", + "G10307A", + "A10745G", + "A11834G", + "A11879G", + "C11976A", + "T12041C", + "G13034A", + "-13189T", + "-13191A" + ], + "F": [ + "L36H" + ], + "G": [ + "P70Q", + "K75R", + "L85S", + "T164S", + "-201N", + "S203D", + "D204Q", + "Q205T", + "A226Y", + "Y227N", + "N228A", + "A229D", + "D230T", + "T231S", + "S233L", + "L234S", + "S235-" + ], + "L": [ + "V50I", + "P1604T" + ], + "SH": [ + "L19I", + "V91I", + "A138T" + ] }, + "labels": { + "aa": "F: L36H; G: P70Q, K75R, L85S, T164S, -201N, S203D, D204Q, Q205T, A226Y, Y227N, N228A, A229D, D230T, T231S, S233L, L234S, S235-; L: V50I, P1604T; SH: L19I, V91I, A138T" + } + }, + "children": [ { - "name": "NODE_0000235", + "name": "NODE_0000264", "node_attrs": { - "div": 0.137, + "div": 0.135, "clade_membership": { "value": "B2" } @@ -31351,147 +32777,135 @@ "branch_attrs": { "mutations": { "nuc": [ - "C4611T" + "T1580C", + "C1628T", + "T1733C", + "A4747G", + "C5772T", + "C6396A", + "C6444T", + "-6863C", + "T6864-", + "C6930T", + "A7141G", + "G12593A" + ], + "M2-1": [ + "K4R" ] + }, + "labels": { + "aa": "M2-1: K4R" } }, "children": [ { - "name": "NODE_0000236", + "name": "NODE_0000265", "node_attrs": { "div": 0.137, "clade_membership": { "value": "B2" } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T6893C", - "T6898C" - ] - } - }, - "children": [ - { - "name": "PP947580", - "node_attrs": { - "div": 0.14, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A579G", - "C1140T", - "G1685A", - "A1691G", - "C1868T", - "C3246T", - "C3837A", - "T4386C", - "A5045G", - "A5542G", - "A5940G", - "-6107A", - "C6189-", - "C6190-", - "A6191-", - "T6192-", - "A6193-", - "A6194-", - "T6195C", - "-6196C", - "T6201-", - "C6202T", - "C6204T", - "T6205A", - "G6206A", - "A6207T", - "A6208C", - "T6209A", - "-6210C", - "-6211T", - "-6212A", - "-6213A", - "-6214A", - "-6215T", - "T6330C", - "T6441C", - "T6571C", - "A6585G", - "T6661C", - "C6678T", - "T6792C", - "C6812T", - "T6903C", - "G6931A", - "T6965-", - "A6966-", - "T6967-", - "A6968-", - "T6969-", - "A6970-", - "A6971-", - "A6972-", - "-6975A", - "-6976T", - "-6977A", - "-6978T", - "-6979A", - "-6980A", - "-6981A", - "-6982A", - "-6983T", - "-6984A", - "A6986-", - "T8653A", - "G9020A", - "A9431T", - "G10346A", - "C11724T", - "C12014T", - "C12455T", - "T12599C", - "A12833G", - "C12848T", - "A12893G" + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A750G", + "G966A", + "-2947A", + "A2949T", + "T2950A", + "A2952T", + "T2954G", + "G2955T", + "T2956C", + "T2958A", + "A2959T", + "T2960A", + "A2961T", + "T2962A", + "A2963-", + "C4107T", + "C4230T", + "T6065C", + "G6244A", + "A6411G", + "T6507C", + "T6624C", + "T6633C", + "T8580C", + "C8936T", + "G9020A", + "A9812G" + ] + } + }, + "children": [ + { + "name": "OP904118", + "node_attrs": { + "div": 0.139, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T1020C", + "T1038C", + "T1122C", + "T1186C", + "C1440T", + "A1856T", + "G3315A", + "C3627T", + "T4889C", + "T5168C", + "A5877G", + "T5965C", + "G6432A", + "C6530T", + "C6621T", + "C6639T", + "T7268C", + "T8795A", + "A9065T", + "A9170G", + "G9236A", + "T9467C", + "T9491C", + "T9512C", + "A9683G", + "A10039G", + "C10215A", + "T10358C", + "C10518T", + "A10820G", + "A11117G", + "C11297T", + "C11498T" ], "G": [ - "S109P", - "S139P", - "T189I", - "-201N", - "N202S", - "S203D", - "D204Q", - "Q205T", - "A226Y", - "Y227N", - "N228T", - "A229D", - "D230T", - "T231S", - "S233L", - "L234S", - "S235-" + "T95I" ], "L": [ - "I496N" + "N543K", + "N958S", + "L1017I", + "P1118S" ], "SH": [ - "N17D" + "Y158H" ] }, "labels": { - "aa": "G: S109P, S139P, T189I, -201N, N202S, S203D, D204Q, Q205T, A226Y, Y227N, N228T, A229D, D230T, T231S, S233L, L234S, S235-; L: I496N; SH: N17D" + "aa": "G: T95I; L: N543K, N958S, L1017I, P1118S; SH: Y158H" } } }, { - "name": "NODE_0000237", + "name": "NODE_0000266", "node_attrs": { "div": 0.138, "clade_membership": { @@ -31501,23 +32915,41 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1098C", - "C3252T", - "T4934C", - "A6106C", - "C6108-", - "A6333G", - "A6357G", - "T9113C", - 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"C5400T", + "A6032T", + "A6553T" ], "F": [ - "S76N", - "T489I" + "I506M" ], "G": [ - "S193P" - ], - "L": [ - "M1839T" - ], - "N": [ - "K359R" - ], - "P": [ - "A77T" + "T103S" ], "SH": [ - "K180E" + "K180I" ] }, "labels": { - "aa": "F: S76N, T489I; G: S193P; L: M1839T; N: K359R; P: A77T; SH: K180E" + "aa": "F: I506M; G: T103S; SH: K180I" } } }, { - "name": "OP904084", + "name": "NODE_0000267", "node_attrs": { "div": 0.139, "clade_membership": { @@ -31596,39 +32989,81 @@ "branch_attrs": { "mutations": { "nuc": [ - "T534C", - "A690G", - "C6153T", - "G6314A", - "C6535T", - "T6579A", - "C7004A", - "G7019A", - "T8669C", - "G9020A", - "T10967C", - "C12030A", - "T12038C" + "G1586A", + "C3233A", + "G5886A", + "G5935A", + "A6545G", + "A7123-", + "G7125A", + "A7126G", + "T7129A", + "A7130T", + "G7132A", + "A7133G", + "G7135A", + "A7136G", + "A7137-", + "G7138-", + "C7139-", + "T7140A", + "G7141A", + "A7142G", + "A7143T", + "-7144T", + "-7145G", + "-7146A", + "-7147A", + "G12896A", + "T13040C" + 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S175N; L: V1351A" - } - } - }, - { - "name": "NODE_0000270", + "name": "NODE_0000281", "node_attrs": { "div": 0.142, "clade_membership": { @@ -34028,18 +34452,17 @@ "branch_attrs": { "mutations": { "nuc": [ - "G6121A", - "C6136A", - "T7851C", - "A11168G" + "T3216A", + "C8684T", + "C10022A" ] } }, "children": [ { - "name": "PP947658", + "name": "PP947614", "node_attrs": { - "div": 0.143, + "div": 0.142, "clade_membership": { "value": "B2" } @@ -34047,29 +34470,16 @@ "branch_attrs": { "mutations": { "nuc": [ - "G2159A", - "A5907G", - "T6661C", - "T6753C", - "A7306G", - "G12998A" - ], - "G": [ - "S139P" - ], - "L": [ - "K47R" + "A2449G", + "A8876G" ] - }, - "labels": { - "aa": "G: S139P; L: K47R" } } }, { - "name": "NODE_0000271", + "name": "PP947564", "node_attrs": { - "div": 0.143, + "div": 0.142, "clade_membership": { "value": "B2" } @@ -34077,21 +34487,49 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6189-", - "A6191T", - "T6192A", - "A6193T", - "T6195A", - "-6196T", - "T12746C" + 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"clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T10959C" - ] - } - } - }, - { - "name": "NODE_0000273", - "node_attrs": { - "div": 0.143, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A762G", - "C1104T", - "G1850A", - "C4625T", - "G6797A", - "T9630C" - ], - "F": [ - "P525L" - ], - "G": [ - "S183R", - "N184K", - "R185E", - "R186A", - "E187T" - ] - }, - "labels": { - "aa": "F: P525L; G: S183R, N184K, R185E, R186A, E187T" - } - }, - "children": [ - { - "name": "PP947603", - "node_attrs": { - "div": 0.144, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T6549C", - "G12070A" - ], - "L": [ - "S1635N" - ] - }, - "labels": { - "aa": "L: S1635N" - } - } - }, - { - "name": "PP947578", - "node_attrs": { - "div": 0.143, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": {} - } - } + "branch_attrs": { + "mutations": { + "nuc": [ + "C6902T" ] } - ] - }, + } + } + ] + }, + { + "name": "NODE_0000284", + "node_attrs": { + "div": 0.141, + "clade_membership": { + "value": "B2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ { - "name": "NODE_0000274", + "name": "PP947670", "node_attrs": { - "div": 0.143, + "div": 0.141, "clade_membership": { "value": "B2" } @@ -34206,453 +34590,57 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1826C", - "T6092C", - "T8918C", - "T11096C", - "T11132C" + "T11856C" ] } + } + }, + { + "name": "PP947570", + "node_attrs": { + "div": 0.142, + "clade_membership": { + "value": "B2" + } }, - "children": [ - { - "name": "PP947579", - "node_attrs": { - "div": 0.144, - "clade_membership": { - "value": "B2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A1337G", - "C3957T", - "G6345A", - "A7596G", - "G9797A", - "A12695G", - "T12965C" - ], - "L": [ - "S144G" - ] - }, - "labels": { - "aa": "L: S144G" - } - } - }, - { - "name": 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W97Q, D101S, S104L, T106P, E110A, G111S, H112P, L113S, H114E, G116E, T117P, P119S, A123T, A125N, T129S, T130V, H133S, T140S, T141R, E142T, T148V, T149H, E150K, K152N, R155S, A156T, T157V, K159R, R161Q, R166A, S169K, T170A, T173R, Q174A, N177L, N180S, S183G, A185R, E187T, D191V, R194D, T195S, Q204E, R207S, T209N, E210P, P214A, T220-, E221-, K222-, T224-, T229S, L233N, S234Q; L: F4L, C5N, V50I, M65N, I89V, S109T, N132S, V141S, N228S, V307K, S314L, I320V, K389R, A429T, V445E, K482R, A505T, Q512L, R513K, C525N, R534S, I537V, I761L, L902I, D907E, V952I, N954A, R963S, *1108V, N1110D, K1129R, V1150T, V1156I, K1175R, I1239L, V1431I, V1475I, V1539A, E1553D, S1572F, S1605I, F1610V, S1635N, D1641N, S1643A, T1653I, I1684M, N1740S, I1768V, N1784D, I1825V, R1873K, S1883A, K1915R, K1916R, I1927V, K1942T; M: D111E; M2-1: L37I, K149R; M2-2: K18E, K22V; N: T54A, K96R, S106N, E110D, F201M, R356K, M385V, N389S; P: K28R, S30P, G31S, V39I, I46V, K57R, S62T, N74K, S75G, T81E, E82V, T86I, T88V, S118P, V122T, S130P, E279D, G286E, E287D; SH: E14K, Q18H, N21K, T22I, N66T, T73S, T80V, I82T, P84T, N89D, V90I, H101Y, R113K, H115S, K123T, I124T, M133E, N134D, T138N, D139N, E142K, A145D, D148R, T153S, R159H, A161V, -175H, *178I, E179D, I180E, R182Q, L183S, S184*", + "aa": "F: I122V, G139N, Q143K, A185D, I286V, R348K, P404N, I449V, R450K, K479R, L503S, T504S, S507L, I511F, R518K, G533N; G: F14L, K17R, I18V, R23A, S24R, Y28F, R29K, T32S, L38I, A58T, T60S, K61E, T62S, C65H, A66T, A71T, S74N, K76E, M79T, A83D, N86D, T87I, K88N, S94P, T98S, S104L, L105N, E110A, G111S, Y114E, G116E, T118A, P119S, S126R, Q128S, T129S, K132R, L136Q, R138S, S139K, T140S, Q143K, Q146P, K151R, K152N, T154P, R155S, T157V, T158S, K159R, R161Q, E162S, Q174A, V177L, N184K, A185R, S186P, E187T, A191V, N195S, S201N, S202H, Q204E, E210P, P211Q, S212A, P214A, P218Q, N227S, S234Q, S235T; L: D4L, C5N, V50I, V55I, R61K, S109T, N132S, V141S, V189I, N228S, K282R, V307K, S314L, Y317H, I320V, S342C, A429T, V445E, Q500R, R513K, C525N, R534S, K619R, L857I, S896V, L902I, D907E, I949L, V952I, N954A, N1110D, V1116T, N1134T, V1150T, K1175R, K1211R, I1239L, I1378M, R1437K, V1475I, I1481V, V1539A, F1602L, A1629T, D1641N, N1643A, I1674V, I1684M, N1740S, I1768V, A1807T, V1821K, I1825V, R1873K, S1883A, I1927V, K1942T; M: D111E, I156T, S241T; M2-1: L37I, K52R, I108V; M2-2: K18E, K22V, A28V, N41A, S55N; N: T54A, C71S, S106N, E110D, V201M, R356K, M385V, N389S, D391N; P: I19L, K28R, S30P, G31S, T35S, V39I, I46V, K57R, R60K, K61P, L65S, S74K, S75G, T81E, P88V, T89M, V92I, S116L, F118P, V122T, S130P, E221D, E279D, G286E; SH: K2I, R8K, E14K, N17T, Q18H, K25D, T73S, T80V, I82T, R83K, P84T, P86L, L88H, V90I, L94F, H101Y, N103D, D108K, K116R, K123T, I124T, G131K, T136K, D139N, E141D, D148R, R159H, K160T, A161V, -179D, K180E, R182Q, L183S", "clade": "A" } }, @@ -36105,81 +36162,78 @@ "mutations": { "nuc": [ "A11G", - "G12A", - "C129T", "A174G", "A195G", "A208G", "C259T", "A276G", - "A288G", "A291G", "T318C", "T337C", "A393G", "A435G", "T450C", - "T477C", "T495C", - "T577C", + "T513C", + "C549T", "A597G", "A627G", "A648C", + "C657T", "T660C", "T697C", + "-741A", "T766C", - "T801C", "T843C", "T870C", "G939A", - "C942T", "T990C", "C1020A", "A1056T", - "G1065A", "C1078T", - "A1119G", "C1134T", - "T1137C", - "C1152T", "A1164G", "C1182T", + "A1253T", + "A1422G", + "G1445A", "A1463T", "C1466T", "G1491A", + "A1500G", + "T1511C", "A1526G", "T1577C", "T1593C", "C1607T", "T1613C", - "C1655T", "G1667A", - "C1682T", "C1694T", "C1718T", "A1754G", "C1773T", "A1775G", - "C1868T", "A1887G", + "C1899T", + "C1925T", "G1928A", "A1931G", "A1963G", - "G1970A", "T2003A", "G2009A", + "G2015A", + "G2090A", + "A2098G", "T2176C", "G2231A", "T2305G", "A2320G", "G2329A", - "T2338C", "T2452C", - "A2470G", "G2497A", + "T2533C", "C2689T", "A2704T", - "A2737G", "C2762T", "C2779T", "G2806A", @@ -36188,26 +36242,24 @@ "C2967T", "T2968C", "A2977T", - "T2990C", - "T3016C", "G3037A", "C3038T", "C3085T", - "C3120T", "A3129G", "T3199C", - "A3201G", + "G3207A", + "A3219G", "A3296G", "T3316C", - "C3453A", + "A3330G", + "G3444A", "A3540G", "T3573A", - "G3804A", + "C3741T", "G3834A", "C3837T", "G3867A", "C3882A", - "A3915G", "G3975A", "A4089G", "C4140T", @@ -36216,26 +36268,30 @@ "T4236C", "T4326C", "A4579G", + "C5114T", "T5127C", "A5195G", "G5219T", + "C5240T", "C5246A", - "C5265T", "A5355G", "A5358C", + "C5562T", "C5591T", "A5631G", "T5640C", + "C5649T", "C5713T", "G5752A", "T5856C", "C5895A", "T5896A", - "T5903C", "T5944C", "T5950C", + "A5955T", "C5963T", "A5964G", + "C5972T", "A5998G", "G6001A", "T6022C", @@ -36247,13 +36303,14 @@ "T6089C", "G6091A", "G6121A", - "G6145A", "A6164T", "T6178C", "A6191G", + "T6206C", + "-6213A", "A6214G", - "-6228T", - "A6681T", + "A6228T", + "C6580T", "C6716T", "A6729G", "A6811G", @@ -36269,7 +36326,6 @@ "T7638C", "A7640G", "G7651A", - "G7655A", "C7872T", "T7898C", "G7901A", @@ -36281,27 +36337,27 @@ "T8153C", "C8195T", "A8231T", + "C8249T", "T8255A", "T8258C", - "G8654A", + "T8747C", "T8750C", "A8774G", "C8807T", "T9138C", "T9156C", + "G9371A", "A9443G", "A9479T", "A9480G", + "G9560A", "A9638G", "A9707G", + "A9725G", "C9761T", "C9773T", - "T9800C", - "T9971C", - "G9989A", "C9998T", "G10004A", - "T10028C", "A10036G", "A10044G", "A10073G", @@ -36313,7 +36369,7 @@ "A10259G", "A10262C", "A10274T", - "C10337T", + "G10304A", "T10379C", "T10385C", "T10442C", @@ -36321,7 +36377,6 @@ "A10544G", "C10547A", "G10553A", - "T10557C", "A10562G", "T10604C", "T10646C", @@ -36331,56 +36386,56 @@ "C10853T", "T10950C", "T10955C", - "G11063A", - "C11087T", "A11156G", "C11159T", "A11243G", + "G11285A", "A11309G", "A11360G", + "T11363C", "A11387G", "A11408G", "A11417G", "A11450G", - "C11456T", - "C11682T", "C11723T", - "C11730T", - "A11795G", + "C11756T", + "G11768A", + "T11826C", "A11870G", "A11873G", "G11885A", "C11931A", "T11982C", "A12024G", - "C12025A", "A12034C", "G12101A", "G12194A", "C12224T", - "T12230C", - "T12302C", + "T12240C", "T12317C", - "A12389G", + "T12377A", "A12554G", "T12587C", "T12671C", - "T12674C", "A12707G", + "C12755T", + "T12793C", "C12824T", + "T12845C", "T12881G", + "G12900A", "A12914G", + "T12935C", "C12959A", - "C12962T", "A12969G", - "A12998G", "G13003A", "T13004C", "G13082A", "C13085T", - "T13229C", + "A13257G", "T13275C", "-13300C", + "-13302A", "A13305G", "A13341G" ], @@ -36393,12 +36448,12 @@ "P112S", "T189A", "T219P", - "-227S", - "-232Y" + "*232Y" ], "L": [ "V64I", "K74R", + "V75I", "R162K", "M245I", "I772V", @@ -36407,6 +36462,7 @@ "S1606P", "T1620E", "D1623A", + "V1876A", "I1935V", "S1946N" ], @@ -36424,8 +36480,6 @@ "Y220H" ], "P": [ - "V82I", - "T85A", "I214V", "N239S", "N284S" @@ -36434,8 +36488,10 @@ "A33V", "P74S", "D87N", + "P132S", "D134E", "S135T", + "I137T", "S151P", "S153P", "A157V", @@ -36445,7 +36501,7 @@ ] }, "labels": { - "aa": "F: K82R, I510V; G: N105H, P112S, T189A, T219P, -227S, -232Y; L: V64I, K74R, R162K, M245I, I772V, K957R, T960A, S1606P, T1620E, D1623A, I1935V, S1946N; M: V23I; M2-1: D170E; M2-2: E37D; N: T57A, Y220H; P: V82I, T85A, I214V, N239S, N284S; SH: A33V, P74S, D87N, D134E, S135T, S151P, S153P, A157V, T160I, I169V, E170K", + "aa": "F: K82R, I510V; G: N105H, P112S, T189A, T219P, *232Y; L: V64I, K74R, V75I, R162K, M245I, I772V, K957R, T960A, S1606P, T1620E, D1623A, V1876A, I1935V, S1946N; M: V23I; M2-1: D170E; M2-2: E37D; N: T57A, Y220H; P: I214V, N239S, N284S; SH: A33V, P74S, D87N, P132S, D134E, S135T, I137T, S151P, S153P, A157V, T160I, I169V, E170K", "clade": "A1" } }, @@ -36459,14 +36515,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -36476,18 +36532,20 @@ "G582A", "T1008C", "T1023C", + "A1119G", "T1402C", "A1591G", + "C1868T", "G2245A", "C2327T", "A2530G", "C2941T", "G3543A", + "A3915G", "A4014T", "A4302T", "G4446A", "A4533G", - "T4560C", "A4604G", "A4662G", "T4677A", @@ -36530,7 +36588,6 @@ "A6937T", "C6967T", "A6997G", - "C6999T", "C7021T", "C7028T", "C7035T", @@ -36546,18 +36603,20 @@ "A8996G", "A9068T", "G9812A", + "T10133A", "A10500G", "C10721T", "C10806T", - "A10907G", + "G10931A", "T11042C", + "G11063A", "T11603C", "G11840A", "A12111C", "T12776C", - "T12793C", "A12798G", - "A12837G" + "A12837G", + "C13250T" ], "F": [ "K518R" @@ -36580,7 +36639,6 @@ "L": [ "S436N", "I1112V", - "V1876A", "N1878D", "I1891V" ], @@ -36593,7 +36651,7 @@ ] }, "labels": { - "aa": "F: K518R; G: S98P, S102L, A108S, A110V, D122G, V130A, A166T, T168A, T176A, L177S, K184E, D194N, S215N; L: S436N, I1112V, V1876A, N1878D, I1891V; M2-1: S173P; P: L52S, K115R" + "aa": "F: K518R; G: S98P, S102L, A108S, A110V, D122G, V130A, A166T, T168A, T176A, L177S, K184E, D194N, S215N; L: S436N, I1112V, N1878D, I1891V; M2-1: S173P; P: L52S, K115R" } } }, @@ -36608,22 +36666,24 @@ "branch_attrs": { "mutations": { "nuc": [ + "C70T", "A126G", "A1766G", "T2326C", "T2966C", "T3568C", "A3605C", + "A3882G", "T4347C", "C4368A", "A4371G", - "G4401A", "T4443C", "A4448G", "A4455G", "C4461T", "A4473G", "G4512A", + "C4560T", "G4562C", "C4578T", "C4581T", @@ -36634,6 +36694,7 @@ "G4667A", "A4687G", "C4688T", + "-4692T", "-4693T", "-4694A", "-4695A", @@ -36676,9 +36737,10 @@ "C5033T", "C5036T", "G5045A", - "T5089C", "A5124G", + "T5177C", "T5623C", + "C5745T", "A5781T", "G5800A", "T5802C", @@ -36704,8 +36766,14 @@ "A6470G", "A6471G", "T6478C", + "A6483G", "A6484G", "C6491T", + "C6499T", + "T6506C", + "A6515G", + "C6523T", + "A6547G", "C6550T", "C6562T", "C6564T", @@ -36715,6 +36783,7 @@ "A6588G", "G6598A", "A6620G", + "T6626C", "T6628C", "C6632T", "A6636C", @@ -36723,17 +36792,14 @@ "C6644A", "A6653C", "A6662C", - "A6674G", "C6680G", "A6685G", "A6695C", "G6698A", - "C6705T", "T6711G", "C6713T", "G6715A", "T6716G", - "T6718C", "G6729T", "C6739T", "C6746T", @@ -36743,7 +36809,6 @@ "G6754A", "C6761G", "C6762T", - "A6763G", "G6766A", "C6774T", "G6783A", @@ -36761,14 +36826,11 @@ "T6852C", "A6859G", "G6862A", - "T6864C", "T6865C", "C6869T", "A6872G", - "A6876G", "G6879A", "G6880A", - "A6895G", "T6896C", "G6897A", "C6898A", @@ -36784,8 +36846,8 @@ "-6909G", "-6910A", "-6911A", - "-6912G", - "-6913G", + "-6912A", + "-6913A", "-6914G", "-6915C", "-6916A", @@ -36805,6 +36867,7 @@ "A6987C", "G6995A", "T6996C", + "T6999C", "C7006T", "A7007G", "A7012G", @@ -36817,7 +36880,6 @@ "G7057A", "C7059T", "T7064C", - "T7065C", "C7069T", "G7082A", "G7084A", @@ -36832,6 +36894,7 @@ "T7122C", "G7146A", "C7205T", + "T7208C", "T7211C", "G7214A", "C7217T", @@ -36841,13 +36904,11 @@ "T7331C", "G7457A", "C7484T", - "C7557T", "T7589C", "C7685T", "A7710G", "T7829C", "G8408A", - "C8414G", "C8441T", "A8444G", "C8489T", @@ -36859,10 +36920,9 @@ "G8636A", "A8678G", "T8817C", - "T8930C", + "T8945C", "C9029T", "C9077T", - "C9092T", "A9098G", "G9347A", "C9431T", @@ -36870,7 +36930,7 @@ "C10871T", "C10877T", "G10886A", - "A10931G", + "G10907A", "A11504G", "T11628C", "C11642T", @@ -36896,17 +36956,22 @@ "S78P", "I80V", "T82I", + "P85S", + "I87T", + "N90S", + "H93Y", + "S101G", "P106S", "S113P", "A118T", "N125S", + "L127P", "S128P", "S129F", "R132T", "S133H", "Q136P", "K139A", - "K143R", "T145S", "T147A", "K150T", @@ -36915,14 +36980,12 @@ "S155R", "T156I", "V157S", - "S158P", "Q161H", "R165W", "T167M", "K169R", "A170T", "P172R", - "R173G", "A174T", "T182I", "G183R", @@ -36937,7 +37000,7 @@ "A208V", "N209S", "A212T", - "M217A", + "M217T", "Q218R", "-220Q", "-221R", @@ -36951,7 +37014,6 @@ "I182V" ], "M2-1": [ - "L118P", "I130V" ], "SH": [ @@ -36964,99 +37026,10 @@ ] }, "labels": { - "aa": "F: D185A, N466S, S504T, S539N; G: A10T, I55M, K57E, T58N, P69S, T71M, N74S, K75R, S78P, I80V, T82I, P106S, S113P, A118T, N125S, S128P, S129F, R132T, S133H, Q136P, K139A, K143R, T145S, T147A, K150T, R151K, I153N, S155R, T156I, V157S, S158P, Q161H, R165W, T167M, K169R, A170T, P172R, R173G, A174T, T182I, G183R, T187S, S193P, T197A, Q200H, N201K, T205A, G206S, S207P, A208V, N209S, A212T, M217A, Q218R, -220Q, -221R, -222K, -223G, -224M, -225E, -226A; L: I182V; M2-1: L118P, I130V; SH: F44L, R96S, D103N, V105A, K108R, L177P" + "aa": "F: D185A, N466S, S504T, S539N; G: A10T, I55M, K57E, T58N, P69S, T71M, N74S, K75R, S78P, I80V, T82I, P85S, I87T, N90S, H93Y, S101G, P106S, S113P, A118T, N125S, L127P, S128P, S129F, R132T, S133H, Q136P, K139A, T145S, T147A, K150T, R151K, I153N, S155R, T156I, V157S, Q161H, R165W, T167M, K169R, A170T, P172R, A174T, T182I, G183R, T187S, S193P, T197A, Q200H, N201K, T205A, G206S, S207P, A208V, N209S, A212T, M217T, Q218R, -220Q, -221R, -222K, -223G, -224M, -225E, -226A; L: I182V; M2-1: I130V; SH: F44L, R96S, D103N, V105A, K108R, L177P" } }, "children": [ - { - "name": "KC562226", - "node_attrs": { - "div": 0.145, - "accession": "KC562226", - "author": { - "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", - "value": 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0.143, + "div": 0.146, + "accession": "KC403980", + "author": { + "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", + "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." + }, "clade_membership": { "value": "A1" + }, + "region": { + "value": "Oceania" + }, + "country": { + "value": "Australia" } }, "branch_attrs": { "mutations": { "nuc": [ - "G1535A", - "T2215A", - "C6068T", - "A6492G", - "C6563T", - "C6655T", - "T6807C", - "A6880G", - "C6967T", - "A7899T", - "T8552C", - "A9305G", - "A10082G", - "T10742C", - "T13064C" + "T87C", + 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N193K, K951N, V1109A, S1111N, H1542Y; SH: K131N" + } + } + }, + { + "name": "NODE_0000289", + "node_attrs": { + "div": 0.143, + "clade_membership": { + "value": "A1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T70C", + "A1119G", + "C1868T", + "G3882A", + "A3915G", + "G4401A", + "A6876G", + "T7065C", + "C7139T", + "C8945T", + "C9092T", + "T10133A", + "G11063A" + ] } }, "children": [ { - "name": "KC562236", + "name": "KC562226", "node_attrs": { - "div": 0.148, - "accession": "KC562236", + "div": 0.147, + "accession": "KC562226", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": 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"value": "China" - }, - "region": { - "value": "Asia" - }, + "div": 0.144, "clade_membership": { "value": "A1" } @@ -37284,336 +37322,802 @@ "branch_attrs": { "mutations": { "nuc": [ - "A15C", - "A117G", - "A237G", - "G270A", - "C477T", - "A498T", - "A609G", - "C666T", - "C909T", - "T1197C", - "A1355G", - "G1376A", - "T1395C", - "A1499G", - "C1577T", - "G1685A", - "A1712G", - "G1963A", - "A1970G", - "A2027G", - "C2148T", - "G2278A", - "G2344T", - "T2468C", - "C2729T", - "G2821T", - "T2943C", - "A3093G", - "G3168A", - "G3270A", - "A3321G", - "A3492G", - "T3523C", - "C3597T", - "A3669G", - "A3675T", - "G3813A", - "T3921C", - "C4050T", - "C4203T", - "G4371A", - "A4494G", - "G4687A", - "A4697T", - "C5028T", - "A5051G", - "T5392C", - "C5393T", - "A5457G", - "G5598A", - "G5706A", - "A5905G", - "T5955C", - "T6043C", - "A6137C", - "T6159G", - "C6196T", - "G6345A", - "C6407A", - "A6416G", - "A6418G", - "G6483A", - "A6497G", - "G6502A", - "T6506C", - "C6523T", - "C6552T", - "G6568A", - "A6594G", 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"children": [ - { - "name": "KC403976", - "node_attrs": { - "div": 0.151, - "accession": "KC403976", - "author": { - "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V.", - "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Wentworth,D.E.,Williams,J.V." - }, - "country": { - "value": "USA" - }, - "region": { - "value": "North America" - }, - "clade_membership": { - "value": "A1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C3827T", - "T5376C", - "T5412C", - "T5429C", - "T5558C", - "T5562C", - "T5577C", - "T5745C", - "T5750C", - "T5834C", - "T5965C", - "T5992C", - "T5999C", - "T6000C", - "T6010C", - "T6013C", - 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"A11162G", - "C12232T", - "G12276A", - "A12383G", - "T12721C" - ], - "F": [ - "I498T" - ], - "L": [ - "F293L", - "P1689L", - "A1704T", - "L1852P" - ], - "M": [ - "H141R", - "M206V" - ] - }, - "labels": { - "aa": "F: I498T; L: F293L, P1689L, A1704T, L1852P; M: H141R, M206V" - } - } - } - ] + "aa": "F: I498T; L: F293L, P1689L, A1704T, L1852P; M: H141R, M206V" } - ] + } } ] } @@ -38234,76 +38292,78 @@ "branch_attrs": { "mutations": { "nuc": [ + "A12G", "A117G", + "T129C", "T138C", "A204G", + "G288A", "G402A", "A411G", "G459A", "T471C", - "C513T", - "T549C", + "C477T", "C564T", - "T657C", - "A741C", + "C577T", + "-741C", "T771C", "A798T", + "C801T", "A816G", "T831C", "T910C", "T927C", + "T942C", "C1044A", + "A1065G", "T1098C", "A1107G", + "C1137T", + "T1152C", "T1186C", - "T1253A", "A1304G", "A1337T", "A1388T", - "G1422A", "A1424C", "C1437T", - "A1445G", "A1448G", - "G1500A", - "C1511T", "G1547A", "C1562T", "A1592G", + "T1655C", + "T1682C", "C1688T", "T1733C", "A1781G", "A1784T", "T1806C", "A1892G", - "T1899C", "G1919A", - "T1925C", "T1964C", + "A1970G", "T1971A", "C1998T", "G2006A", - "A2015G", "T2021C", - "A2090G", "C2093A", - "G2098A", "A2179G", "T2188C", "T2200C", "C2290T", "C2311T", "A2323G", + "C2338T", "A2361G", "C2374A", "A2425G", "T2455C", - "C2533T", + "G2470A", "C2600T", "T2635A", "C2653T", "A2668T", "G2683A", + "G2737A", "T2767C", "C2773T", "C2940A", @@ -38311,22 +38371,23 @@ "T2957C", "T2974C", "A2984G", + "C2990T", + "C3016T", + "T3120C", "A3150G", - "A3207G", - "G3219A", + "G3201A", "T3225C", "T3247C", "C3267T", "T3312C", - "G3330A", - "A3444G", + "A3453C", "C3474T", "G3612A", "C3705T", "A3738G", - "T3741C", "A3756G", "C3778T", + "A3804G", "A3805C", "A3843G", "C3927T", @@ -38342,59 +38403,54 @@ "C4293T", "C4587T", "A5102G", - "T5114C", "C5117T", "T5135C", "T5156C", - "T5240C", + "T5265C", "C5284T", "T5352A", "T5376C", - "T5562C", "C5643A", - "T5649C", "A5704G", "G5706A", "A5730T", "T5754C", "C5868T", "T5887C", + "C5903T", "A5909G", "A5918G", - "T5955A", - "T5972C", "A6044G", "-6048G", "A6069G", "C6072T", "T6076A", + "A6145G", "T6146C", "A6151G", "C6172T", "C6175A", "C6180A", "C6190T", - "C6206T", - "A6213C", - "-6228A", + "-6213C", "G6261A", "C6559A", - "T6580C", "C6680A", + "T6681A", "C6717T", "C6938T", "C6950T", "T7452C", "G7526A", "T7601C", + "A7655G", "T7670C", "A7733C", "A7823G", "A7865G", "T8072A", - "T8249C", "A8393G", - "C8747T", + "A8654G", "A8756G", "A8779G", "T8804A", @@ -38403,31 +38459,32 @@ "T8933C", "T9119C", "T9134C", - "A9371G", "A9461G", "A9471C", - "A9560G", "T9578C", "C9677T", "A9683T", - "G9725A", "G9755A", + "C9800T", "C9803T", "G9920A", + "C9971T", + "A9989G", + "C10028T", "C10121T", - "A10133T", "C10190T", "T10205C", "C10277A", "T10289C", - "A10304G", "G10316A", "T10331C", + "T10337C", "T10358C", "A10370G", "A10433G", "C10457T", "C10556T", + "C10557T", "A10658G", "A10700G", "A10733G", @@ -38437,64 +38494,64 @@ "A10856G", "A10857C", "G10958A", + "T11087C", "T11150A", - "A11285G", - "C11363T", + "T11456C", "C11498T", "A11615G", + "T11682C", + "T11730C", "T11741C", - "T11756C", - "A11768G", + "G11795A", "G11796A", - "C11826T", "T11876C", "A11969G", "T11975C", + "A12025C", "T12038C", "T12056C", "T12080A", "G12113A", "A12140G", "C12203T", - "C12240T", + "C12230T", + "C12302T", "C12305T", "A12326G", - "A12377T", + "G12389A", "A12392C", "T12431C", "A12467G", + "C12674T", "A12686G", "A12695G", "A12745G", - "T12755C", - "C12845T", "C12848T", "A12863G", "T12897C", - "A12900G", - "C12935T", + "T12962C", + "G12998A", "A13046G", "T13049C", "T13163C", "A13193G", "A13196G", + "C13229T", "C13238T", - "T13250C", - "G13257A", "A13259G", "A13295T", "C13296T", "-13300A", - "A13302C" + "-13302C" ], "G": [ "S102P", "K139E", "T145K", + "S227-", "T235I" ], "L": [ - "I75V", "K538R", "D546E", "S769R", @@ -38515,20 +38572,20 @@ ], "P": [ "A59T", + "I82V", + "A85T", "S242T", "D282E" ], "SH": [ "K71E", - "S132P", - "T137I", "N139S", "K142R", "L177S" ] }, "labels": { - "aa": "G: S102P, K139E, T145K, T235I; L: I75V, K538R, D546E, S769R, D1037E, S1506P, V1544I, N1860S, N1912D; M: N66S; M2-1: T183I; M2-2: H35Q; P: A59T, S242T, D282E; SH: K71E, S132P, T137I, N139S, K142R, L177S", + "aa": "G: S102P, K139E, T145K, S227-, T235I; L: K538R, D546E, S769R, D1037E, S1506P, V1544I, N1860S, N1912D; M: N66S; M2-1: T183I; M2-2: H35Q; P: A59T, I82V, A85T, S242T, D282E; SH: K71E, N139S, K142R, L177S", "clade": "A2" } }, @@ -38536,7 +38593,7 @@ { "name": "NODE_0000296", "node_attrs": { - "div": 0.123, + "div": 0.124, "clade_membership": { "value": "A2a" } @@ -38555,6 +38612,7 @@ "A2674G", "T3303C", "T4275C", + "C4560T", "C4688T", "C5970T", "T6081C", @@ -38562,12 +38620,13 @@ "A6695C", "T6711C", "A6970G", + "T6999C", "T7117C", "T7565C", "A8939G", "T8945C", "A10262G", - "A10931G", + "G10907A", "G11372A", "G11786A", "T12044C" @@ -38596,14 +38655,14 @@ "author": "Piyaratna,R.,Tollefson,S.J.,Williams,J.V.,Piyaratna,R.V.", "value": "Piyaratna,R.,Tollefson,S.J.,Williams,J.V.,Piyaratna,R.V." }, - "country": { - "value": "USA" + "clade_membership": { + "value": "A2a" }, "region": { "value": "North America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "USA" } }, "branch_attrs": { @@ -38864,7 +38923,7 @@ { "name": "NODE_0000297", "node_attrs": { - "div": 0.135, + "div": 0.136, "clade_membership": { "value": "A2a" } @@ -39053,8 +39112,7 @@ "L177F", "T179M", "S229P", - "T231I", - "-232*" + "T231I" ], "L": [ "S436N", @@ -39084,14 +39142,14 @@ ] }, "labels": { - "aa": "F: A61S, K143T, V449I; G: T77A, P81S, S101N, T135A, R159S, V171I, P172R, L177F, T179M, S229P, T231I, -232*; L: S436N, I821V, I962V, T1116I; M2-1: N116S; M2-2: D30E; N: T57A; P: V82A, S97F, I280T; SH: V46I, V155A, Y176H, E180*" + "aa": "F: A61S, K143T, V449I; G: T77A, P81S, S101N, T135A, R159S, V171I, P172R, L177F, T179M, S229P, T231I; L: S436N, I821V, I962V, T1116I; M2-1: N116S; M2-2: D30E; N: T57A; P: V82A, S97F, I280T; SH: V46I, V155A, Y176H, E180*" } }, "children": [ { "name": "NODE_0000298", "node_attrs": { - "div": 0.139, + "div": 0.14, "clade_membership": { "value": "A2a" } @@ -39183,14 +39241,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2a" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -39244,20 +39302,20 @@ { "name": "KC403979", "node_attrs": { - "div": 0.141, + "div": 0.142, "accession": "KC403979", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2a" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -39319,7 +39377,7 @@ { "name": "NODE_0000299", "node_attrs": { - "div": 0.136, + "div": 0.137, "clade_membership": { "value": "A2a" } @@ -39341,7 +39399,7 @@ { "name": "NODE_0000300", "node_attrs": { - "div": 0.14, + "div": 0.141, "clade_membership": { "value": "A2a" } @@ -39461,7 +39519,7 @@ { "name": "NODE_0000301", "node_attrs": { - "div": 0.142, + "div": 0.143, "clade_membership": { "value": "A2a" } @@ -39540,7 +39598,7 @@ { "name": "MH150889", "node_attrs": { - "div": 0.142, + "div": 0.143, "clade_membership": { "value": "A2a" } @@ -39556,7 +39614,7 @@ { "name": "MH150888", "node_attrs": { - "div": 0.142, + "div": 0.143, "clade_membership": { "value": "A2a" } @@ -39572,7 +39630,7 @@ { "name": "NODE_0000302", "node_attrs": { - "div": 0.139, + "div": 0.14, "clade_membership": { "value": "A2a" } @@ -39691,14 +39749,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2a" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -39764,7 +39822,7 @@ { "name": "NODE_0000304", "node_attrs": { - "div": 0.142, + "div": 0.143, "clade_membership": { "value": "A2a" } @@ -39822,14 +39880,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2a" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -40086,7 +40144,7 @@ { "name": "NODE_0000305", "node_attrs": { - "div": 0.145, + "div": 0.146, "clade_membership": { "value": "A2a" } @@ -40327,7 +40385,7 @@ { "name": "NODE_0000306", "node_attrs": { - "div": 0.147, + "div": 0.148, "clade_membership": { "value": "A2a" } @@ -40385,14 +40443,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -40462,7 +40520,7 @@ { "name": "NODE_0000307", "node_attrs": { - "div": 0.147, + "div": 0.148, "clade_membership": { "value": "A2a" } @@ -40486,20 +40544,20 @@ { "name": "KJ627390", "node_attrs": { - "div": 0.148, + "div": 0.149, "accession": "KJ627390", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -40553,20 +40611,20 @@ { "name": "KJ627427", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "KJ627427", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -40642,20 +40700,20 @@ { "name": "KJ627416", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "KJ627416", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -40710,7 +40768,7 @@ { "name": "NODE_0000311", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2a" } @@ -40728,20 +40786,20 @@ { "name": "KJ627425", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "KJ627425", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -40791,20 +40849,20 @@ { "name": "KJ627418", "node_attrs": { - "div": 0.148, + "div": 0.149, "accession": "KJ627418", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -40866,7 +40924,7 @@ { "name": "NODE_0000313", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2a" } @@ -40893,14 +40951,14 @@ "author": 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}, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -41023,7 +41081,7 @@ { "name": "NODE_0000315", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2a" } @@ -41045,14 +41103,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -41082,7 +41140,7 @@ { "name": "NODE_0000316", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2a" } @@ -41098,7 +41156,7 @@ { "name": "NODE_0000317", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2a" } @@ -41126,14 +41184,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -41171,7 +41229,7 @@ { "name": "NODE_0000318", "node_attrs": { - "div": 0.149, + "div": 0.15, "clade_membership": { "value": "A2a" } @@ -41211,20 +41269,20 @@ { "name": "KJ627407", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "KJ627407", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -41251,20 +41309,20 @@ { "name": "KJ627388", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "KJ627388", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -41323,20 +41381,20 @@ { "name": "KJ627433", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "KJ627433", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -41402,14 +41460,14 @@ "author": 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}, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2a" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2a" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -41524,7 +41582,7 @@ { "name": "NODE_0000322", "node_attrs": { - "div": 0.128, + "div": 0.129, "clade_membership": { "value": "A2b" } @@ -41566,7 +41624,6 @@ "T4179C", "C4203T", "A4533G", - "T4560C", "T5455C", "G5479T", "A5505G", @@ -41591,7 +41648,6 @@ "A6939G", "C6967T", "A6997G", - "C6999T", "C7028T", "G7061A", "A7097C", @@ -41614,7 +41670,7 @@ "T9872C", "C10058T", "A10859G", - "A10907G", + "G10931A", "A11192G", "A11336G", "G11687A", @@ -41632,6 +41688,7 @@ "T228-", "S229-", "T230-", + "*232-", "N233-", "Q234-" ], @@ -41651,7 +41708,7 @@ ] }, "labels": { - "aa": "G: T82I, A110V, T228-, S229-, T230-, N233-, Q234-; M: K87R; N: V92A; P: V88I, P277L; SH: S9N, E180K", + "aa": "G: T82I, A110V, T228-, S229-, T230-, *232-, N233-, Q234-; M: K87R; N: V92A; P: V88I, P277L; SH: S9N, E180K", "clade": "A2b" } }, @@ -41659,7 +41716,7 @@ { "name": "NODE_0000323", "node_attrs": { - "div": 0.132, + "div": 0.133, "clade_membership": { "value": "A2b1" } @@ -41879,14 +41936,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -41957,14 +42014,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -42054,7 +42111,7 @@ { "name": "NODE_0000326", "node_attrs": { - "div": 0.14, + "div": 0.141, "clade_membership": { "value": "A2b1" } @@ -42275,20 +42332,20 @@ { "name": "KJ627392", "node_attrs": { - "div": 0.144, + "div": 0.145, "accession": "KJ627392", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -42387,20 +42444,20 @@ { "name": "KJ627401", "node_attrs": { - "div": 0.146, + "div": 0.147, "accession": "KJ627401", "author": { "author": 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"Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -42459,7 +42516,7 @@ { "name": "NODE_0000329", "node_attrs": { - "div": 0.144, + "div": 0.145, "clade_membership": { "value": "A2b1" } @@ -42578,20 +42635,20 @@ { "name": "KJ627385", "node_attrs": { - "div": 0.145, + "div": 0.146, "accession": "KJ627385", "author": { "author": 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"country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -43039,7 +43096,7 @@ { "name": "NODE_0000335", "node_attrs": { - "div": 0.145, + "div": 0.146, "clade_membership": { "value": "A2b1" } @@ -43051,20 +43108,20 @@ { "name": "KJ627412", "node_attrs": { - "div": 0.145, + "div": 0.146, "accession": "KJ627412", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -43104,14 +43161,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -43137,20 +43194,20 @@ { "name": "KJ627420", "node_attrs": { - "div": 0.146, + "div": 0.147, "accession": "KJ627420", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -43188,7 +43245,7 @@ { "name": "NODE_0000337", "node_attrs": { - "div": 0.133, + "div": 0.134, "clade_membership": { "value": "A2b1" } @@ -43344,14 +43401,14 @@ "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -43385,7 +43442,7 @@ { "name": "NODE_0000339", "node_attrs": { - "div": 0.143, + "div": 0.144, "clade_membership": { "value": "A2b1" } @@ -43466,20 +43523,20 @@ { "name": "MK989732", "node_attrs": { - "div": 0.146, + "div": 0.147, "accession": "MK989732", "author": { "author": "Phan,M.V.T.,Agoti,C.N.,Nokes,D.J.,Cotten,M.", "value": "Phan,M.V.T.,Agoti,C.N.,Nokes,D.J.,Cotten,M." }, - "country": { - "value": "Kenya" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "Africa" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Kenya" } }, "branch_attrs": { @@ -43558,14 +43615,14 @@ "author": "Phan,M.V.T.,Agoti,C.N.,Nokes,D.J.,Cotten,M.", "value": "Phan,M.V.T.,Agoti,C.N.,Nokes,D.J.,Cotten,M." }, - "country": { - "value": "Kenya" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "Africa" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Kenya" } }, "branch_attrs": { @@ -43669,7 +43726,7 @@ { "name": "NODE_0000340", "node_attrs": { - "div": 0.139, + "div": 0.14, "clade_membership": { "value": "A2b1" } @@ -43809,20 +43866,20 @@ { "name": "KC562224", "node_attrs": { - "div": 0.141, + "div": 0.142, "accession": "KC562224", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -43906,7 +43963,7 @@ { "name": "NODE_0000343", "node_attrs": { - "div": 0.142, + "div": 0.143, "clade_membership": { "value": "A2b1" } @@ -43952,67 +44009,67 @@ }, "children": [ { - "name": "KC403984", + "name": "KC403983", "node_attrs": { "div": 0.143, - "accession": "KC403984", + "accession": "KC403983", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Australia" } }, "branch_attrs": { "mutations": { "nuc": [ - "A1292G", - "A4682T", - "T4683A", - "A4687C", - "C4688-", - 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+ "value": "Australia" } }, "branch_attrs": { "mutations": { "nuc": [ - "A1119G", - "T6807C" + "A1292G", + "A4682T", + "T4683A", + "A4687C", + "C4688-", + "A4689-", + "A4690-", + "A4691-", + "-4717A", + "-4718A", + "-4719A", + "C11351T" ] } } @@ -44022,7 +44079,7 @@ { "name": "NODE_0000344", "node_attrs": { - "div": 0.145, + "div": 0.146, "clade_membership": { "value": "A2b1" } @@ -44279,7 +44336,7 @@ { "name": "NODE_0000346", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b1" } @@ -44458,7 +44515,7 @@ { "name": "NODE_0000348", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b1" } @@ -44830,7 +44887,7 @@ { "name": "NODE_0000350", "node_attrs": { - "div": 0.149, + "div": 0.15, "clade_membership": { "value": "A2b1" } @@ -44964,7 +45021,7 @@ { "name": "NODE_0000351", "node_attrs": { - "div": 0.15, + "div": 0.151, "clade_membership": { "value": "A2b1" } @@ -45020,7 +45077,7 @@ { "name": "KY474529", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b1" } @@ -45160,7 +45217,7 @@ { "name": "KY474537", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b1" } @@ -45189,7 +45246,7 @@ { "name": "KY474530", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b1" } @@ -45225,7 +45282,7 @@ { "name": "NODE_0000353", "node_attrs": { - "div": 0.14, + "div": 0.141, "clade_membership": { "value": "A2b1" } @@ -45261,20 +45318,20 @@ { "name": "KC403978", "node_attrs": { - "div": 0.143, + "div": 0.144, "accession": "KC403978", "author": { "author": "Lorenzi,H.,Town,C.,Halpin,R.,Nguyen,A.,Bera,J.,Fedorova,N.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Mackay,I.M.,Sloots,T.P.,Nissen,M.D.,Wentworth,D.E.,Williams,J.V.", "value": 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"country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -45716,14 +45773,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -45855,7 +45912,7 @@ { "name": "NODE_0000360", "node_attrs": { - "div": 0.144, + "div": 0.145, "clade_membership": { "value": "A2b1" } @@ -46067,7 +46124,7 @@ { "name": "NODE_0000362", "node_attrs": { - "div": 0.15, + "div": 0.151, "clade_membership": { "value": "A2b1" } @@ -46096,7 +46153,7 @@ { "name": "KY474538", "node_attrs": { - "div": 0.153, + "div": 0.154, "clade_membership": { "value": "A2b1" } @@ -46176,7 +46233,7 @@ { "name": "KY474533", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b1" } @@ -46269,14 +46326,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": 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"country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -46754,7 +46811,7 @@ { "name": "NODE_0000368", "node_attrs": { - "div": 0.147, + "div": 0.148, "clade_membership": { "value": "A2b1" } @@ -46806,14 +46863,14 @@ "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -46879,20 +46936,20 @@ { "name": "KJ627429", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "KJ627429", "author": { "author": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E.", "value": "Wentworth,D.E.,Halpin,R.A.,Bera,J.,Lin,X.,Fedorova,N.,Tsitrin,T.,McLellan,M.,Stockwell,T.,Amedeo,P.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Schobel,S.,Shrivastava,S.,Garcia,J.,Laguna-Torres,V.A.,Leguia,M.,Benavides,J.G.,Halsey,E." }, - "country": { - "value": "Peru" + "clade_membership": { + "value": "A2b1" }, "region": { "value": "South America" }, - "clade_membership": { - "value": "A2b1" + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -46933,14 +46990,14 @@ 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"NODE_0000381", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -48115,20 +48172,20 @@ { "name": "MW221987", "node_attrs": { - "div": 0.148, + "div": 0.149, "accession": "MW221987", "author": { "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2b2" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2b2" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -48167,7 +48224,7 @@ { "name": "NODE_0000382", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -48184,7 +48241,7 @@ { "name": "OP904069", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -48200,7 +48257,7 @@ { "name": "OP904059", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -48227,7 +48284,7 @@ { "name": "NODE_0000383", "node_attrs": { - "div": 0.14, + "div": 0.141, "clade_membership": { "value": "A2b2" } @@ -48243,7 +48300,7 @@ { "name": "MZ504958", "node_attrs": { - "div": 0.147, + "div": 0.148, "clade_membership": { "value": "A2b2" } @@ -48472,7 +48529,7 @@ { "name": "MK588634", "node_attrs": { - "div": 0.15, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -48659,20 +48716,20 @@ { "name": "MW221986", "node_attrs": { - "div": 0.149, + "div": 0.15, "accession": "MW221986", "author": { "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." }, - "country": { - "value": "Australia" + "clade_membership": { + "value": "A2b2" }, "region": { "value": "Oceania" }, - "clade_membership": { - "value": "A2b2" + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -48799,7 +48856,7 @@ { "name": "OP904054", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -48872,7 +48929,7 @@ { "name": "OP904051", "node_attrs": { - "div": 0.149, + "div": 0.15, "clade_membership": { "value": "A2b2" } @@ -48981,7 +49038,7 @@ { "name": "NODE_0000389", "node_attrs": { - "div": 0.146, + "div": 0.147, "clade_membership": { "value": "A2b2" } @@ -49034,7 +49091,7 @@ { "name": "NODE_0000390", "node_attrs": { - "div": 0.15, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -49124,7 +49181,7 @@ { "name": "OP904058", "node_attrs": { - "div": 0.15, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -49212,7 +49269,7 @@ { "name": "MZ504962", "node_attrs": { - "div": 0.151, + "div": 0.152, "clade_membership": { "value": "A2b2" } @@ -49315,7 +49372,7 @@ { "name": "NODE_0000393", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -49376,20 +49433,20 @@ { "name": "MH828684", "node_attrs": { - "div": 0.154, + "div": 0.155, "accession": "MH828684", 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"clade_membership": { + "value": "A2b2" }, "region": { "value": "Asia" }, - "clade_membership": { - "value": "A2b2" + "country": { + "value": "Vietnam" } }, "branch_attrs": { @@ -49863,7 +49920,7 @@ { "name": "NODE_0000395", "node_attrs": { - "div": 0.143, + "div": 0.144, "clade_membership": { "value": "A2b2" } @@ -49882,7 +49939,7 @@ { "name": "NODE_0000396", "node_attrs": { - "div": 0.147, + "div": 0.144, "clade_membership": { "value": "A2b2" } @@ -49890,92 +49947,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "T91C", - "T201C", - "G315A", - "C585T", - "T660C", - "C831T", - "A1116G", - "G1397A", - "C1733T", - "G1781A", - "G1892A", - "C2076A", - "C2228T", - "G2536A", - "A2632G", - "A2848G", - "A2952G", - "T4080G", - "C4116T", - "C4557T", - "C4961T", - "G5102A", - "C5543T", - "C5568A", - "T5796C", - "C5950T", - "G6063A", - "C6141T", - "A6142G", - "A6546T", - "C6550T", - "T6583C", - "C6590T", - "A6724G", - "C6760T", - "G6783T", - "G6790A", - "C6887T", - "A6973G", - "A7023G", - 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}, "children": [ { - "name": "MN867464", + "name": "NODE_0000414", "node_attrs": { - "div": 0.145, - "accession": "MN867464", - "author": { - "author": "Li,X.,Kong,M.,Zou,M.,Guo,L.,Su,X.", - "value": "Li,X.,Kong,M.,Zou,M.,Guo,L.,Su,X." - }, - "country": { - "value": "China" - }, - "region": { - "value": "Asia" - }, + "div": 0.144, "clade_membership": { "value": "A2b2" } @@ -50359,62 +51449,220 @@ "mutations": { "nuc": [ "G105A", - "C1773T", - "A1922G", - "A2579G", - "A3547G", - "G3894A", - "C4467T", - "T4784C", - "T6072C", - "A6429G", - "C6486T", - "C6596T", - "A6616G", - "G6623A", - "T6626C", - "T6718C", - "G6742A", - "C6761T", - "T7037A", - "A7055G", - "C7078T", - "C7521T", - "T9026A", - "C10268A", - "T10541C", - "G12695A", - "T12956C", - "A13329G" - ], - "F": [ - "K166E" - ], - "G": [ - "P117L", - "T124A", - "R126H", - "L127P", - "S158P", - "A166T", - "P172L" - ], - "L": [ - "N620K" - ], - "M": [ - "K139E" + "C1773T" ] + } + }, + "children": [ + { + "name": "MN867464", + 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T124A, R126H, L127P, S158P, A166T, P172L; L: N620K; M: K139E" + { + "name": "MK588633", + "node_attrs": { + "div": 0.151, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T87C", + "G144T", + "G282A", + "G313A", + "A579G", + "G819A", + "A873G", + "T1033C", + "T1140C", + "A1262G", + "T1538G", + "T2030A", + "T2096C", + "T2290C", + "A2500T", + "C2947T", + "G3204A", + "T3453C", + "T3552C", + "A3774T", + "G3975A", + "C4059T", + "A4089G", + "G4194A", + "T4281C", + "A4590C", + "G4796A", + "T4985C", + "A5087G", + "A5210G", + "A5220G", + "G5297A", + "C5472T", + "C5547T", + "G5752A", + "A5931G", + "A6135G", + "T6159C", + "A6212C", + "A6216G", + "A6243G", + "G6258A", + "T6441C", + "T6489C", + "A6509C", + "C6530T", + "T6531C", + "T6583C", + "G6610A", + "A6744G", + "T6807C", + "T6836C", + "T6843C", + "T6864C", + "C6935A", + "T6978C", + "C7106T", + "G7739A", + "C7775T", + "C7851T", + "T7889C", + "A8705T", + "A9275G", + "C9395T", + "C9473T", + 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"C9944T", + "A11420G", + "A12254G" ] } }, "children": [ { - "name": "MK588633", + "name": "NODE_0000417", "node_attrs": { - "div": 0.15, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -50460,171 +51772,37 @@ "branch_attrs": { "mutations": { "nuc": [ - "T87C", - "G105A", - "G144T", - "G282A", - "G313A", - "A579G", - "G819A", - "A873G", - "T1033C", - "T1140C", - "A1262G", - "T1538G", - "C1773T", - "T2030A", - "T2096C", - "T2290C", - "A2500T", - "C2947T", - "G3204A", - "T3453C", - "T3552C", - "A3774T", - "G3975A", - "C4059T", - "A4089G", - "G4194A", - "T4281C", - "A4590C", - "G4796A", - "T4985C", - "A5087G", - "A5210G", - "A5220G", - "G5297A", - "C5472T", - "C5547T", - "G5752A", - "A5931G", - "A6135G", - "T6159C", - "A6212C", - "A6216G", - "A6243G", - "G6258A", - "T6441C", - "T6489C", - "A6509C", - "C6530T", - "T6531C", - "T6583C", - "G6610A", - "A6744G", - "T6807C", - "T6843C", - "T6864C", - "C6935A", - "T6978C", - "C7106T", - "G7739A", - "C7775T", - "C7851T", - "A8705T", - 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"nuc": [ - "A1089T", - "A1385G", - "A1430G", - "T1520C", - "A2949G", - "T3468C", - "G3756A", - "C4467T", - "C6449T", - "C6511A", - "A6589C", - "C7096T", - "C7098G", - "G7334A", - "T9068A", - "G9878A", - "A9920G", - "G10481A", - "T11552C", - "G11693A" - ], - "G": [ - "S68F", - "P89T", - "T115P" + "V105A" ] }, "labels": { - "aa": "G: S68F, P89T, T115P" + "aa": "P: P130Q; SH: V105A" } }, "children": [ { - "name": "OR338754", + "name": "KY474539", "node_attrs": { - "div": 0.147, + "div": 0.152, "clade_membership": { "value": "A2b2" } @@ -50632,69 +51810,75 @@ "branch_attrs": { "mutations": { "nuc": [ - "T246C", - "G1233A", - "A1526G", - "T1613C", - "T1725C", - "A1814G", - "T2531C", - "A3478G", - "G4038A", - "A4611T", - "C5400T", - "T5452C", - "T5802C", - "C5920T", - "C6405T", - "T6736C", - "A6781G", - "T6864C", - "T6978C", - "T6999C", - "T7025C", - "T7028C", - "C7646T", - "A8095T", - "A8423G", - "C8489T", - "G10552A", - "A10751G", - "T12092C", - "C12336T", - "G12593A", - "A12742G", - 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"NODE_0000418", "node_attrs": { - "div": 0.145, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -50702,18 +51886,58 @@ "branch_attrs": { "mutations": { "nuc": [ - "A96G", - "G3315A", + "T1438C", + "G1781A", + "T2509C", + "T3405C", "C3621T", - "A9914T" + "C4272T", + "G4416A", + "C4521A", + "G4575A", + "T4587C", + "A4617G", + "T4874C", + "A6315T", + "T6491C", + "T6531C", + "T6607C", + "T6711C", + "T6716C", + "T6864C", + "C6946T", + "G7523A", + "G7655A", + "A9821G", + "C10101T", + "C10430T", + "C10513T", + "C11288T", + "G11342A", + "C12650T", + "G13145A" + ], + "G": [ + "I82T", + "S121P", + "V157A" + ], + "L": [ + "T1116I" + ], + "P": [ + "L64S" ] + }, + "labels": { + "aa": "G: I82T, S121P, V157A; L: T1116I; P: L64S" } }, "children": [ { - "name": "MZ504967", + "name": "NODE_0000419", "node_attrs": { - "div": 0.15, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -50721,120 +51945,103 @@ "branch_attrs": { "mutations": { "nuc": [ - "C78T", - "G177A", - "A250C", - 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- "L": [ - "T505A", - "M1609I" - ], - "P": [ - "L277P" - ] }, - "labels": { - "aa": "G: L41M, K150R, S162F, R183T, A216T; L: T505A, M1609I; P: L277P" - } - }, - "children": [ { - "name": "NODE_0000416", + "name": "NODE_0000421", "node_attrs": { - "div": 0.147, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -51689,27 +52153,30 @@ "branch_attrs": { "mutations": { "nuc": [ - "G825A", - "A2149G", - "T2752C", - "A4877G", - "T5541C", - "C6068T", - "C6977A", - "C8309T", - "G9371A", - "G9806A", - "C9944T", - "A11420G", - "A12254G" + "G1376A", + "T1437C", + "A2964G", + "T3177C", + "G3756A", + "T3924A", + "G4020A", + "A8093G", + "T8570C", + "G8779A" + ], + "L": [ + "R538K" ] + }, + "labels": { + "aa": "L: R538K" } }, "children": [ { - "name": "NODE_0000417", + "name": "NODE_0000422", "node_attrs": { - "div": 0.148, + "div": 0.15, "clade_membership": { "value": "A2b2" } @@ -51717,37 +52184,46 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1200T", - "C1636A", - "G4152A", - "T5807C", - "T5880C", - "A8111G", - "A8744G", - "A9146G", - "C10868A", - "A12281G", - "T12323C", - "G12893A", - "A12983G", - "G13249A" + "C2148T", + "T2970C", + "A4572G", + "C4688-", + "T6149C", + "T6330C", + "C6449T", + "T6524C", + "T6621C", + "T6843C", + "T7013C", + "A7087G", + "G7488A", + "G9722A", + "T9774C", + "G10481A", + "T11006G", + "T11262A", + "G12254A", + "G12410A", + "G13183A" ], - "P": [ - "P130Q" + "G": [ + "S68F", + "L93P" ], - "SH": [ - "V105A" + "L": [ + "G108S", + "S1366T" ] }, "labels": { - "aa": "P: P130Q; SH: V105A" + "aa": "G: S68F, L93P; L: G108S, S1366T" } }, "children": [ { - "name": "KY474539", + "name": "OP904094", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -51755,73 +52231,61 @@ "branch_attrs": { "mutations": { "nuc": [ - "C477T", - "T486C", - "T495C", - "C624A", - "C903T", - "A1442G", - "C1829T", - "T2461C", - "C2710T", - "G2937A", - "G3171A", - "C3379T", - "T3795A", - "A4035G", - "T4356C", - "C4650T", - "C5309T", - "G5526A", - "G5817A", - "A6120C", - "G6121A", - "T6198C", - "T6403C", - "A6560G", - "C6602T", + "G204A", + "T207C", + "C1200T", + "C1433T", + "T1435C", + "T1472C", + "T1520C", + "T1538C", + "T1562C", + "T2148G", + "G2149A", + "A2150-", + "A2569T", + "A2743G", + "C2967T", + "A3822G", + "G3834A", + "A3942G", + "T4320C", + "-4688T", + "C4919T", + "C5240T", + "A6397G", + "T6531C", + "T6660C", "C6717T", - "G6753A", - "C6794T", - "A6943G", - "G6974A", - "A7086G", - "C7283T", - "C7812A", - "A8084T", - "A8162G", - "T9101C", - "C9804T", - "A9932T", - "G10658A", - "T11036A", - "T11442C", - "T11465C", - "T11535C", - "C12635T", - "A12926G", - "G13185T" - ], - "F": [ - "L110F" + "A6765G", + "C7121A", + "C7313T", + "G7463A", + "A7526G", + "G7739A", + "A7787G", + "C7890T", + "G8654A", + "G10553A", + "A12020G", + "C12044T", + "T12689A", + "A13055G" ], "G": [ - "Y53H", - "N105S", - "S119L", - "T183I" + "I51V" ], - "M2-2": [ - "P21L" + "P": [ + "I63T" ] }, "labels": { - "aa": "F: L110F; G: Y53H, N105S, S119L, T183I; M2-2: P21L" + "aa": "G: I51V; P: I63T" } } }, { - "name": "NODE_0000418", + "name": "NODE_0000423", "node_attrs": { "div": 0.151, "clade_membership": { @@ -51831,58 +52295,43 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1438C", - "G1781A", - "T2509C", - "T3405C", - "C3621T", - "C4272T", - "G4416A", - "C4521A", - "G4575A", - "T4587C", - "A4617G", - "T4874C", - "A6315T", - "T6491C", - "T6531C", - "T6607C", - "T6711C", - "T6716C", - "T6864C", - "C6946T", - "G7523A", - "G7655A", - "A9821G", - "C10101T", - "C10430T", - "C10513T", - "C11288T", - "G11342A", - "C12650T", - "G13145A" + "T3105C", + "A4687-", + "A4689-", + "A4690-", + "A4691-", + "-4714A", + "-4715A", + "-4716T", + "-4717A", + "-4718A", + "-4719A", + "T5967C", + "T6078C", + "G6364A", + "A6899T", + "A9210C", + "A9260G", + "T11084C", + "T11240C", + "G11951A", + "G12062A", + "A13052G" ], "G": [ - "I82T", - "S121P", - "V157A" - ], - "L": [ - "T1116I" - ], - "P": [ - "L64S" + "A40T", + "Q218L" ] }, "labels": { - "aa": "G: I82T, S121P, V157A; L: T1116I; P: L64S" + "aa": "G: A40T, Q218L" } }, "children": [ { - "name": "NODE_0000419", + "name": "PP947649", "node_attrs": { - "div": 0.152, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -51890,103 +52339,80 @@ "branch_attrs": { "mutations": { "nuc": [ - "C610T", - "C973T", - "T1406A", - "T1472C", - "T1492C", - "T1511C", - "T1520C", - "C1540T", - "T1541C", - "G1685A", - "A2069G", - "C3858T", - "T4683-", - "A4684-", - "A4685-", - "A4686-", - "A4687-", - "C4688-", - "A4689-", - "A4690-", - "A4691-", - "-4710A", - "-4711T", - "-4712A", - "-4713A", - "-4714A", - "-4715A", - "-4716C", - "-4717A", - "-4718A", - "-4719A", - "T5844C", - "T6026C", - "T6030C", - "C6146T", - "C6504T", - "T6633C", - "T6635C", - "C6655T", - "G6668A", - "C6837T", - "A7321G", - "A8156G", - "A9713G", - "T12005A" + "G1330A", + "C1412T", + "T2033C", + "G2090A", + "G2758A", + "C2840T", + "G2964A", + "G3019A", + "T3121C", + "A3450G", + "C3621T", + "G4305A", + "C4491T", + "G4549A", + "T4587C", + "G5241A", + "G5526A", + "G5566A", + "T5589C", + "G5918A", + "A6003G", + "A6074G", + "C6348T", + "A6423G", + "C6761T", + "T6852C", + "T6864C", + "T6869C", + "T6940C", + "G6968A", + "A7020G", + "A7108G", + "A7307G", + "T7988C", + "G8627A", + "A9821G", + "A10601T", + "A11078G", + "T11261C", + "C11381T", + "G11969A", + "C12650T", + "G12659A", + "T12860C", + "T12959C", + "T13258C" + ], + "F": [ + "V500I" ], "G": [ - "V130A", - "P137S", - "R141K" + "P172L", + "V208A" ], - "L": [ - "N52S" + "M2-1": [ + "A169T" ], "P": [ - "V82A", - "T98I" + "R28K" ], "SH": [ - "I178T" + "D25N", + "R142K" ] }, "labels": { - "aa": "G: V130A, P137S, R141K; L: N52S; P: V82A, T98I; SH: I178T" - } - }, - "children": [ - { - "name": "OY757646", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "OY757611", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } + "aa": "F: V500I; G: P172L, V208A; M2-1: A169T; P: R28K; SH: D25N, R142K" } - ] + } }, { - "name": "NODE_0000420", + "name": "NODE_0000424", "node_attrs": { - "div": 0.151, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -51994,18 +52420,62 @@ "branch_attrs": { "mutations": { "nuc": [ - "C2024T", - "C2148G", - "G2149A", - "A2150-" + "T976C", + "C987T", + "G1970A", + "T3354C", + "T3486C", + "C3849T", + "C5321T", + "T5586C", + "T5757C", + "A5768G", + "C6539T", + "C6720T", + "A6745G", + "G6757A", + "C6836T", + "T7091C", + "C7619T", + "A8134C", + "A8819G", + "C9059T", + "A9305T", + "C10610T", + "T10652A", + "A10873G", + "A12220G", + "G12516A" + ], + "G": [ + "S98F", + "T183I", + "R184T", + "T197I" + ], + "L": [ + "N323T", + "H1162Q", + "K1236R", + "K1685R", + "D1784N" + ], + "M2-2": [ + "T25I" + ], + "SH": [ + "Q92R" ] + }, + "labels": { + "aa": "G: S98F, T183I, R184T, T197I; L: N323T, H1162Q, K1236R, K1685R, D1784N; M2-2: T25I; SH: Q92R" } }, "children": [ { - "name": "OP904125", + "name": "OP904092", "node_attrs": { - "div": 0.151, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -52013,72 +52483,45 @@ "branch_attrs": { "mutations": { "nuc": [ - "A4289G", - "T5153A", - "A6588G", - "G6684A", - "T6999C" - ], - "F": [ - "Q413R" - ], - "G": [ - "R184T" + "T2148G", + "G2149A", + "A2150-", + "-4687A", + "-4688T", + "-4689A", + "-4690A", + "-4691A", + "A4714-", + "A4715-", + "T4716-", + "A4717-", + "A4718-", + "A4719-" ] - }, - "labels": { - "aa": "F: Q413R; G: R184T" } } }, { - "name": "OP904045", + "name": "MW221989", "node_attrs": { - "div": 0.152, + "div": 0.153, + "accession": "MW221989", + "author": { + "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", + "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." + }, "clade_membership": { "value": "A2b2" + }, + "region": { + "value": "Oceania" + }, + "country": { + "value": "Australia" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A3333G", - "T3502C", - "C3858T", - "A4931G", - "T6403C", - "T6463C", - "T6489C", - "T6575C", - "T6626C", - "T6633C", - "T6643C", - "T6730C", - "C6770T", - "T6940C", - "G7009A", - "T7709C", - "C8936T" - ], - "G": [ - "Y53H", - "S73P", - "V110A", - "L127P", - "S133P", - "F162L", - "S164P", - "T183R", - "R184N", - "R185I", - "T187S", - "A188T", - "T189A" - ] - }, - "labels": { - "aa": "G: Y53H, S73P, V110A, L127P, S133P, F162L, S164P, T183R, R184N, R185I, T187S, A188T, T189A" - } + "mutations": {} } } ] @@ -52088,9 +52531,9 @@ ] }, { - "name": "NODE_0000421", + "name": "NODE_0000425", "node_attrs": { - "div": 0.148, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -52098,77 +52541,33 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1376A", - "T1437C", - "A2964G", - "T3177C", - "G3756A", - "T3924A", - "G4020A", - "A8093G", - "T8570C", - "G8779A" + "T6730C" ], - "L": [ - "R538K" + "G": [ + "F162L" ] }, "labels": { - "aa": "L: R538K" + "aa": "G: F162L" } }, "children": [ { - "name": "NODE_0000422", + "name": "NODE_0000426", "node_attrs": { - "div": 0.15, + "div": 0.149, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C2148T", - "T2970C", - "A4572G", - "C4688-", - "T6149C", - "T6330C", - "C6449T", - "T6524C", - "T6621C", - "T6843C", - "T7013C", - "A7087G", - "G7488A", - "G9722A", - "T9774C", - "G10481A", - "T11006G", - "T11262A", - "G12254A", - "G12410A", - "G13183A" - ], - "G": [ - "S68F", - "L93P" - ], - "L": [ - "G108S", - "S1366T" - ] - }, - "labels": { - "aa": "G: S68F, L93P; L: G108S, S1366T" - } + "mutations": {} }, "children": [ { - "name": "OP904094", + "name": "LC789936", "node_attrs": { - "div": 0.153, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -52176,63 +52575,120 @@ "branch_attrs": { "mutations": { "nuc": [ - "G204A", - "T207C", - "C1200T", - "C1433T", - "T1435C", - "T1472C", - "T1520C", - "T1538C", - "T1562C", - "T2148G", - "G2149A", - "A2150-", - "A2569T", - "A2743G", - "C2967T", - "A3822G", - "G3834A", - "A3942G", - "T4320C", - "-4688T", - "C4919T", - "C5240T", - "A6397G", - "T6531C", - "T6660C", - "C6717T", - "A6765G", - "C7121A", - "C7313T", - "G7463A", - "A7526G", - "G7739A", - "A7787G", - "C7890T", - "G8654A", - "G10553A", - "A12020G", + "G411A", + "T1421C", + "G1439A", + "G1589A", + "G1787A", + "C1829T", + "C1847T", + "G1865A", + "T2600C", + "G2937A", + "C2941T", + "T2963C", + "G2964A", + "C2967A", + "G3315A", + "G4023A", + "C4272T", + "T4320A", + "C4398A", + "C4434T", + "C4688T", + "-4692A", + "-4693C", + "-4694A", + "-4695A", + "-4696A", + "-4697A", + "-4698T", + "A4720-", + "T4721-", + "G5009A", + "C5156T", + "A5274G", + "G5328A", + "C5664T", + "T5748C", + "C5864T", + "C6348T", + "G6376A", + "T6489C", + "C6495T", + "C6499T", + "C6595T", + "T6635C", + "T6682C", + "T6704C", + "T6711C", + "T6937C", + "T6940C", + "C7094T", + "A7688G", + "A7727G", + "C7763T", + "A7790T", + "T8180C", + "C8264T", + "G8408A", + "C8489T", + "A8705T", + "A8740G", + "T9008C", + "A9009G", + "A9128G", + "A9212G", + "A9314G", + "A9641G", + "A9938G", + "T10492G", + "A10598G", + "T10628C", + "A10757G", + "A11099G", + "T11390C", + "A11411G", + "G11541A", + "C11931A", "C12044T", - "T12689A", - "A13055G" + "G12104A", + "T12605C", + "C12635T", + "T12902C", + "C12987T" ], "G": [ - "I51V" + "A44T", + "P85S", + "P117S", + "V130A", + "S146P", + "I153T" ], - "P": [ - "I63T" + "L": [ + "K513N", + "N525S", + "I615V", + "V1109G", + "V1459I" + ], + "M2-1": [ + "S180G" + ], + "SH": [ + "T124I" ] }, "labels": { - "aa": "G: I51V; P: I63T" + "aa": "G: A44T, P85S, P117S, V130A, S146P, I153T; L: K513N, N525S, I615V, V1109G, V1459I; M2-1: S180G; SH: T124I" } } }, { - "name": "NODE_0000423", + "name": "NODE_0000427", "node_attrs": { - "div": 0.151, + "div": 0.149, "clade_membership": { "value": "A2b2" } @@ -52240,43 +52696,16 @@ "branch_attrs": { "mutations": { "nuc": [ - "T3105C", - "A4687-", - "A4689-", - "A4690-", - "A4691-", - "-4714A", - "-4715A", - 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A188T, T189A; L: S1538L, V1615I; P: T54I, R79G; SH: P153T" } } }, { - "name": "NODE_0000424", + "name": "KY474532", "node_attrs": { - "div": 0.153, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -52365,120 +52794,80 @@ "branch_attrs": { "mutations": { "nuc": [ - "T976C", - "C987T", - "G1970A", - "T3354C", - "T3486C", - "C3849T", - "C5321T", - "T5586C", - "T5757C", - "A5768G", - "C6539T", - "C6720T", - "A6745G", - "G6757A", - "C6836T", - "T7091C", - "C7619T", - "A8134C", + "C1104T", + "A2057G", + "T2060C", + "A2625G", + "C4134T", + "A4685G", + "C4688-", + "A4689-", + "A4690-", + "A4691-", + "-4710A", + "-4711T", + "-4712A", + "-4713A", + "-4714A", + "-4715A", + "-4716C", + "-4717A", + "-4718A", + "-4719A", + "A4790G", + "C5126T", + "A5129G", + "T5177C", + "A6135C", + "C6136-", + "T6330C", + "T6643C", + "T6718C", + "G6797A", + "G6800A", + "C6834A", + "A6838G", + "C6887T", + "T7103A", "A8819G", - "C9059T", - "A9305T", - "C10610T", - "T10652A", - "A10873G", - "A12220G", - 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"N1038D", + "N1878S", + "K1884R" + ], + "M2-2": [ + "S17N" + ], + "SH": [ + "D69E", + "V155I" ] + }, + "labels": { + "aa": "F: I510V, P520T; G: T58A, V130A, L162S, A174V, H202Y, A214T; L: A508T, N1038D, N1878S, K1884R; M2-2: S17N; SH: D69E, V155I" } - ] + } }, { - "name": "NODE_0000428", + "name": "NODE_0000429", "node_attrs": { - "div": 0.149, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -52820,31 +53035,43 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1835T", - "T4074C", - "G5368A", - "C6564T", - "C6717T", - "G6790A", - "A6811T", - "A10787G", - "C11741T" + "A594G", + "A873G", + "C1718T", + "C4140A", + "T4722C", + "A5355G", + "A6024G", + "A6373G", + "C6542T", + "A7131T", + "A7141G", + "A7143G", + "G9461A", + "A10495G", + "T10769C", + "A11186G", + "C12105T", + "A12947T", + "T13136C", + "A13212G" ], "G": [ - "A182T", - "T189S" + "I43V", + "T99I", + "S128P" ], - "M2-2": [ - "A41T" + "L": [ + "D1110G" ] }, "labels": { - "aa": "G: A182T, T189S; M2-2: A41T" + "aa": "G: I43V, T99I, S128P; L: D1110G" } }, "children": [ { - "name": "PP947655", + "name": "PP947631", "node_attrs": { "div": 0.155, "clade_membership": { @@ -52854,125 +53081,85 @@ "branch_attrs": { "mutations": { "nuc": [ - "C24A", - "G417A", - "G1550A", - "C1559A", - "C2117T", - "G2194A", - "A2299G", - "G2380A", - "T2668C", - "C2689A", - "G3114A", - "C3189T", - "C3273T", - "C3652T", - "C4284A", - "A4332G", - "T4404C", - "T4443C", - "A4579G", - "G4596A", - "C4609A", - "C5147T", - "G5297A", - "T5700G", - "A5706G", - "G5956A", - "C6012T", - "T6061C", - "C6130T", - "C6348T", - "A6418G", - "T6441C", - "C6720T", - "C6730T", - "T6731C", - "C6762A", - "C6767T", - "A6801G", - "C6850T", - "T6864C", - "T6885C", - "G6886A", - "T6940C", - "T6983C", - "T6992C", - "T6999C", - "T7025C", - "T7028C", - "T7037C", - "T7053C", - "T7075C", - "C7295T", - "T7638C", - "A8201G", - "G8336A", - "C8342T", - "T8348A", - "C8670T", - "G8688A", - "G8996A", - "T9551C", - "C9765T", - "A9827G", - "A10278G", - "T11081C", - 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"R184G", + "T205A", + "M217I" ], "L": [ - "A508T", - "N1038D", - "N1878S", - "K1884R" - ], - "M2-2": [ - "S17N" + "T429A" ], "SH": [ - "D69E", - "V155I" + "P74S", + "S115N", + "R142I", + "S151L" ] }, "labels": { - "aa": "F: I510V, P520T; G: T58A, V130A, L162S, A174V, H202Y, A214T; L: A508T, N1038D, N1878S, K1884R; M2-2: S17N; SH: D69E, V155I" + "aa": "G: R184G, T205A, M217I; L: T429A; SH: P74S, S115N, R142I, S151L" } } }, { - "name": "NODE_0000429", + "name": "NODE_0000430", "node_attrs": { - "div": 0.15, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -52980,45 +53167,27 @@ "branch_attrs": { "mutations": { "nuc": [ - "A594G", - "A873G", - "C1718T", - "C4140A", - "T4722C", - "A5355G", - "A6024G", - "A6373G", - "C6542T", - "A7131T", - "A7141G", - "A7143G", - "G9461A", - "A10495G", - "T10769C", - "A11186G", - "C12105T", - "A12947T", - "T13136C", - "A13212G" - ], - "G": [ - "I43V", - "T99I", - "S128P" + "C286T", + "A861G", + "C3621A", + "G6783A", + "C7088T", + "T7432C", + "G9989A" ], "L": [ - "D1110G" + "V89A" ] }, "labels": { - "aa": "G: I43V, T99I, S128P; L: D1110G" + "aa": "L: V89A" } }, "children": [ { - "name": "PP947631", + "name": "PP947616", "node_attrs": { - "div": 0.154, + "div": 0.152, "clade_membership": { "value": "A2b2" } @@ -53026,83 +53195,33 @@ "branch_attrs": { "mutations": { "nuc": [ - "C24T", - "T600C", - "A651T", - "T1047C", - "G1065A", - "T1083C", - "T1122C", - "A3087G", - "A3276G", - "C3312T", - "G3528A", - "A3732G", - "G3996A", - "C4551T", - "G4940A", - "C4961T", - "G5382A", - "T5610A", - "C5713T", - "G5837A", - "C5916T", - "G5918T", - "C5945T", - "C6055T", - "C6288T", - "T6330C", - "C6378T", - "G6627A", + "C1152T", + "C2419T", + "T2665C", + "C2947T", + "C3006T", + "T4182C", + "G6024A", "T6628C", - "A6669G", - "A6796G", - "A6816G", - "A6855G", - "A6859G", - "G6897A", - "C7139T", - "G7427A", - "T8420C", - "A8451G", - "C8480T", - "T9272C", - "T9671C", - "T9774C", - "G9794A", - "T9824C", - "G9857A", - "T11027C", - "A11213G", - "A11561G", - "T11996C", - "C12056T", - "T12290C", - "G13249A", - "T13335C" - ], - "G": [ - "R184G", - "T205A", - "M217I" + "A6876G", + "C6932T", + "C7550T", + "A8471G", + "T10607C", + "C11724T", + "T11982A" ], "L": [ - "T429A" - ], - "SH": [ - "P74S", - "S115N", - "R142I", - "S151L" + "S1606T" ] }, "labels": { - "aa": "G: R184G, T205A, M217I; L: T429A; SH: P74S, S115N, R142I, S151L" + "aa": "L: S1606T" } } }, { - "name": "NODE_0000430", + "name": "NODE_0000431", "node_attrs": { "div": 0.151, "clade_membership": { @@ -53112,27 +53231,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C286T", - "A861G", - "C3621A", - "G6783A", - "C7088T", - "T7432C", - "G9989A" - ], - "L": [ - "V89A" + "T1613C" ] - }, - "labels": { - "aa": "L: V89A" } }, "children": [ { - "name": "PP947616", + "name": "PP947598", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -53140,35 +53247,63 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1152T", - "C2419T", - "T2665C", - "C2947T", - "C3006T", - "T4182C", - "G6024A", - "T6628C", - "A6876G", - "C6932T", - "C7550T", - "A8471G", - "T10607C", - "C11724T", - "T11982A" + "G316A", + "T906C", + "A1586T", + "A4488G", + "G5058A", + "C5537T", + "A5843G", + "A6194G", + "-6224A", + "C6225T", + "A6227-", + "A6228-", + "A6229-", + "A6230-", + "T6231-", + "A6232-", + "A6474G", + "A6519G", + "G6753A", + "C6794T", + "T6864C", + "C6877A", + "T7178C", + "T7565C", + "A11527T", + "C12431T" + ], + "G": [ + "T183I", + "Q211K" ], "L": [ - "S1606T" + "K1454I" + ], + "M2-1": [ + "V108I" + ], + "N": [ + "V93I" + ], + "P": [ + "E113D" + ], + "SH": [ + "T15I", + "N117S" ] }, "labels": { - "aa": "L: S1606T" + "aa": "G: T183I, Q211K; L: K1454I; M2-1: V108I; N: V93I; P: E113D; SH: T15I, N117S" } } }, { - "name": "NODE_0000431", + "name": "NODE_0000432", "node_attrs": { - "div": 0.151, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -53176,15 +53311,39 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1613C" + "C585T", + "T636C", + "G819A", + "A885G", + "C960T", + "C1428T", + "A4943G", + "G5837A", + "C6327T", + "T6531C", + "C6730T", + "T6940C", + "G7137A", + "C8366T", + "G11285A", + "A12366C" + ], + "P": [ + "P61S" + ], + "SH": [ + "S115N" ] + }, + "labels": { + "aa": "P: P61S; SH: S115N" } }, "children": [ { - "name": "PP947598", + "name": "PP947671", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -53192,63 +53351,47 @@ "branch_attrs": { "mutations": { "nuc": [ - "G316A", - "T906C", - "A1586T", - "A4488G", - "G5058A", - "C5537T", - "A5843G", - "A6194G", - "-6224A", - "C6225T", - "A6227-", - "A6228-", - "A6229-", - "A6230-", - "T6231-", - "A6232-", - "A6474G", - "A6519G", - "G6753A", - "C6794T", - "T6864C", - "C6877A", - "T7178C", - "T7565C", - "A11527T", - "C12431T" + "C1607T", + "A6593T", + "C6596A", + "A6598-", + "C6599-", + "A6600-", + "T6601-", + "C6602-", + "A6603-", + "A6604-", + "C6605-", + "A6606-", + "T6607-", + "C6608-", + "A6609-", + "G6610-", + "A6611-", + "C6612-", + "A6613-", + "C6614T", + "C6720T", + "A12485G" ], "G": [ - "T183I", - "Q211K" - ], - "L": [ - "K1454I" - ], - "M2-1": [ - "V108I" - ], - "N": [ - "V93I" - ], - "P": [ - "E113D" - ], - "SH": [ - "T15I", - "N117S" + "T118-", + "S119-", + "T120-", + "S121-", + "D122-", + "T123-" ] }, "labels": { - "aa": "G: T183I, Q211K; L: K1454I; M2-1: V108I; N: V93I; P: E113D; SH: T15I, N117S" + "aa": "G: T118-, S119-, T120-, S121-, D122-, T123-" } } }, { - "name": "NODE_0000432", + "name": "PP947620", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -53256,106 +53399,16 @@ "branch_attrs": { "mutations": { "nuc": [ - "C585T", - "T636C", - "G819A", - "A885G", - "C960T", - "C1428T", - "A4943G", - "G5837A", - "C6327T", - "T6531C", - "C6730T", - "T6940C", - "G7137A", - "C8366T", - "G11285A", - "A12366C" - ], - "P": [ - "P61S" + "G6364A" ], - "SH": [ - "S115N" + "G": [ + "A40T" ] }, "labels": { - "aa": "P: P61S; SH: S115N" - } - }, - "children": [ - { - "name": "PP947671", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1607T", - "A6593T", - "C6596A", - "A6598-", - "C6599-", - "A6600-", - "T6601-", - "C6602-", - "A6603-", - "A6604-", - "C6605-", - "A6606-", - "T6607-", - "C6608-", - "A6609-", - "G6610-", - "A6611-", - "C6612-", - "A6613-", - "C6614T", - "C6720T", - "A12485G" - ], - "G": [ - "T118-", - "S119-", - "T120-", - "S121-", - "D122-", - "T123-" - ] - }, - "labels": { - "aa": "G: T118-, S119-, T120-, S121-, D122-, T123-" - } - } - }, - { - "name": "PP947620", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G6364A" - ], - "G": [ - "A40T" - ] - }, - "labels": { - "aa": "G: A40T" - } - } + "aa": "G: A40T" } - ] + } } ] } @@ -53370,11 +53423,42 @@ ] } ] + } + ] + }, + { + "name": "NODE_0000433", + "node_attrs": { + "div": 0.147, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A2085C", + "A3153T", + "C4563T", + "A6332G", + "C13216A" + ], + "G": [ + "K29R" + ], + "P": [ + "I280L" + ] }, + "labels": { + "aa": "G: K29R; P: I280L" + } + }, + "children": [ { - "name": "NODE_0000433", + "name": "PP315925", "node_attrs": { - "div": 0.147, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -53382,28 +53466,222 @@ "branch_attrs": { "mutations": { "nuc": [ - "A2085C", - "A3153T", - "C4563T", - "A6332G", - "C13216A" + "A11G", + "G12A", + "A23C", + "C24-", + "A167G", + "A168G", + "A174G", + "C379T", + "T618C", + "G619A", + "G825A", + "T843C", + "A1077G", + "A1119G", + "T1401C", + "T1452C", + "T1480C", + "T1520C", + "T1613C", + "A1649G", + "G1661A", + "T1676C", + "T1755C", + "A2175G", + "C2257T", + "T2665C", + "A2932G", + "A2955G", + "T3016C", + "A3373G", + "G3513A", + "T3552C", + "G4095A", + "G4634A", + "A4835C", + "T5089C", + "C5376T", + "G5391A", + "G5598A", + "T5623C", + "G5629A", + "A5886G", + "C5907T", + "C5940T", + "G6114A", + "A6257G", + "C6549T", + "A6597G", + "A6598C", + "G6750A", + "C6898A", + "A6899G", + "A6900C", + "T6904A", + "G6906T", + "-6907A", + "-6908G", + "G7044A", + "A7428G", + "A7445G", + "C8264T", + "A8267G", + "T8453C", + "T8738C", + "T9551C", + "T9677C", + "A9869G", + "A9870C", + "A10016C", + "A10017C", + "A10025G", + "A10026G", + "A10277C", + "A10279G", + "G10451A", + "T10538C", + "A10544G", + "C10784A", + "A11051G", + "C11456T", + "A11457G", + "A11528G", + "C11723T", + "T11778G", + "A11780G", + "T11949C", + "T11982C", + "T12129C", + "A12356G", + "G12818A", + "G12893A", + "G12913A", + "T12959C", + "A12966G", + "T13031C", + "G13183A", + "C13228G", + "T13229C" + ], + "F": [ + "I108V", + "S528N" + ], + "G": [ + "K4R", + "T118P" + ], + "L": [ + "N88D", + "I902L", + "L950F", + "K951Q", + "T954A", + "E1037D", + "N1038S", + "I1431V", + "S1538A", + "S1606P", + "R1916K", + "K1934E" + ], + "M": [ + "Y4C" + ], + "M2-1": [ + "R33S", + "L118P" + ], + "N": [ + "E43G", + "A194T" + ], + "P": [ + "I78T" + ], + "SH": [ + "F44L", + "V46I", + "N107K", + "K108D" + ] + }, + "labels": { + "aa": "F: I108V, S528N; G: K4R, T118P; L: N88D, I902L, L950F, K951Q, T954A, E1037D, N1038S, I1431V, S1538A, S1606P, R1916K, K1934E; M: Y4C; M2-1: R33S, L118P; N: E43G, A194T; P: I78T; SH: F44L, V46I, N107K, K108D" + } + } + }, + { + "name": "NODE_0000434", + "node_attrs": { + "div": 0.15, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G837A", + "C1718T", + "A1994T", + "A2093T", + "C3930T", + "A4604G", + "T5117C", + "C5156T", + "C5240T", + "A6125G", + "T6139C", + "A6515G", + "A6835G", + "G6997A", + "G7057A", + "T7075A", + "T7697C", + "A8156G", + "T8378C", + "A8633C", + "A8765G", + "G9365A", + "A9480G", + "G10485A", + "G10844A", + "A11117T", + "G11228A", + "C11642T", + "A12029G", + "G12467A", + "T12623C", + "A13178G", + "A13239G" + ], + "F": [ + "K518R" ], "G": [ - "K29R" + "N90S", + "T197A" + ], + "L": [ + "I772V", + "V1107I" ], "P": [ - "I280L" + "E282D" ] }, "labels": { - "aa": "G: K29R; P: I280L" + "aa": "F: K518R; G: N90S, T197A; L: I772V, V1107I; P: E282D" } }, "children": [ { - "name": "PP315925", + "name": "NODE_0000435", "node_attrs": { - "div": 0.154, + "div": 0.15, "clade_membership": { "value": "A2b2" } @@ -53411,222 +53689,29 @@ "branch_attrs": { "mutations": { "nuc": [ - "A11G", - "G12A", - "A23C", - "C24-", - "A167G", - "A168G", - "A174G", - "C379T", - "T618C", - "G619A", - "G825A", - "T843C", - "A1077G", - "A1119G", - "T1401C", - "T1452C", - "T1480C", - "T1520C", - "T1613C", - "A1649G", - "G1661A", - "T1676C", - "T1755C", - "A2175G", - "C2257T", - "T2665C", - "A2932G", - "A2955G", - "T3016C", - "A3373G", - "G3513A", - "T3552C", - "G4095A", - "G4634A", - "A4835C", - "T5089C", - "C5376T", - "G5391A", - "G5598A", - "T5623C", - "G5629A", - "A5886G", - "C5907T", - "C5940T", - "G6114A", - "A6257G", - "C6549T", - "A6597G", - "A6598C", - "G6750A", - "C6898A", - "A6899G", - "A6900C", - "T6904A", - "G6906T", - "-6907A", - "-6908G", - "G7044A", - "A7428G", - "A7445G", - "C8264T", - "A8267G", - "T8453C", - "T8738C", - "T9551C", - "T9677C", - "A9869G", - "A9870C", - "A10016C", - "A10017C", - "A10025G", - "A10026G", - "A10277C", - "A10279G", - "G10451A", - "T10538C", - "A10544G", - "C10784A", - "A11051G", - "C11456T", - "A11457G", - "A11528G", - "C11723T", - "T11778G", - "A11780G", - "T11949C", - "T11982C", + "A6619G", + "C6655T", + "C6825T", + "G6862A", + "C9512T", "T12129C", - "A12356G", - "G12818A", - "G12893A", - "G12913A", - "T12959C", - "A12966G", - "T13031C", - "G13183A", - "C13228G", - "T13229C" - ], - "F": [ - "I108V", - "S528N" - ], - "G": [ - "K4R", - "T118P" - ], - "L": [ - "N88D", - "I902L", - "L950F", - "K951Q", - "T954A", - "E1037D", - "N1038S", - "I1431V", - "S1538A", - "S1606P", - "R1916K", - "K1934E" - ], - "M": [ - "Y4C" - ], - "M2-1": [ - "R33S", - "L118P" - ], - "N": [ - "E43G", - "A194T" - ], - "P": [ - "I78T" - 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+ ], + "G": [ + "N105D" + ], + "L": [ + "I1107T" ], "SH": [ - "S68P" + "T85I" ] }, "labels": { - "aa": "SH: S68P" + "aa": "G: N105D; L: I1107T; SH: T85I" } }, "children": [ { - "name": "NODE_0000443", + "name": "NODE_0000444", "node_attrs": { - "div": 0.15, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -54488,36 +54582,105 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1847T", - "G1955A", - "G3035A", - "C3117T", - "C5747T", - "A6559G", - "G7019A", - "T7031C", - "C8921T", - "T10014C", - "T10486C", - "T11648A" + "T213C", + "A393G", + "G489A", + "C814T", + "A1155T", + "T1421C", + "A1679G", + "A1971G", + "T2060C", + "T2437C", + "T2773C", + "T2860A", + "A2932G", + "A2945G", + "G3207A", + "T3279C", + "A3525G", + "T3568C", + "A4242G", + "G4353A", + "T4530A", + "C4653T", + "C4919T", + "G4940A", + "T4949C", + "A5180G", + "G5219A", + "G5598A", + "C5714T", + "T5868C", + "T5883C", + "T5929C", + "A6034G", + "A6057G", + "T6441C", + "A6615T", + "T6660C", + "G6665A", + "A6669C", + 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"T1421C", - "A1679G", - "A1971G", - "T2060C", - "T2437C", - "T2773C", - "T2860A", - "A2932G", - "A2945G", - "G3207A", - "T3279C", - "A3525G", - "T3568C", - "A4242G", - "G4353A", - "T4530A", - "C4653T", - "C4919T", - "G4940A", - "T4949C", - "A5180G", - "G5219A", - "G5598A", - "C5714T", - "T5868C", - "T5883C", - "T5929C", - "A6034G", - "A6057G", - "T6441C", - "A6615T", - "T6660C", - "G6665A", - "A6669C", - "G6710A", - "T6711C", - "G6766A", - "G6830T", - "C6958T", - "T6990C", - "A7101G", - "C7118T", - "A7253G", - "C7619T", - "G7694A", - "G7739A", - "A8057G", - "C8123T", - "A8418G", - "A8451G", - "G8723A", - "C9155T", - "C9489T", - "A9494G", - "G9584A", - "G9695A", - "C9908T", - "G10004A", - "A10931G", - "A11231C", - "C11244T", - "C12464T", - "C12623T", - "G12977A", - "A13101G" - ], - "G": [ - "S140N", - "R141S", - "S155N", - "A174T", - "S195I" - ], - "L": [ - "I418V", - "T429A", - "K1355N", - "I1979V" - ], - "P": [ - "T242A" - ], - "SH": [ - "P74L", - "T181A" + "C2148-" ] + } + } + }, + { + "name": "MW221993", + "node_attrs": { + "div": 0.156, + "accession": "MW221993", + "author": { + "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", + "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." }, - "labels": { - "aa": "G: S140N, R141S, S155N, A174T, S195I; L: I418V, T429A, K1355N, I1979V; P: T242A; SH: P74L, T181A" + "clade_membership": { + "value": "A2b2" + }, + "region": { + "value": "Oceania" + }, + "country": { + "value": "Australia" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A4687-", + "C4688-", + "A4689-", + "A4690-", + "A4691-" + ] + } + } + } + ] + }, + { + "name": "NODE_0000445", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G36A", + "G954A", + "G1304A", + "A1334G", + "T2311C", + "A2815C", + "G2944A", + "C2962T", + "C3621T", + "C5135T", + "C6000T", + "T6172C", + "C6558T", + "C6887T", + "C7006T", + "A7020C", + "A7481G", + "C8309T", + "G8903A", + "A9020G", + "G9794A", + "T11282C", + "G11951A", + "A13209G" + ], + "G": [ + "A214V" + ] + }, + "labels": { + "aa": "G: A214V" + } + }, + "children": [ + { + "name": "NODE_0000446", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A5054G" + ] } }, "children": [ { - "name": "OP904145", + "name": "OP345084", "node_attrs": { - "div": 0.156, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -54635,26 +54800,56 @@ "branch_attrs": { "mutations": { "nuc": [ - "C2148-" + "C903T", + "T2338C", + "C3735T", + "A3938G", + "T4539C", + "T5174C", + "C5754T", + "G5817A", + "C6012T", + "T6246C", + "A6445T", + "G6610T", + "G6766A", + "A7164G", + "G7370A", + "C8304T", + "C9206T", + "A9410G", + "A9713G", + "A9893G", + "T9923C", + "G10350A", + "A10502G", + "C10514T", + "A11462G", + "A11942G" + ], + "F": [ + "K296R" + ], + "G": [ + "S67C", + "D122Y", + "A174T" + ], + "L": [ + "M68I", + "V1062I", + "I1112M" ] + }, + "labels": { + "aa": "F: K296R; G: S67C, D122Y, A174T; L: M68I, V1062I, I1112M" } } }, { - "name": "MW221993", + "name": "NODE_0000447", "node_attrs": { - "div": 0.156, - "accession": "MW221993", - "author": { - "author": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S.", - "value": "Tulloch,R.L.,Kok,J.,Carter,I.,Dwyer,D.E.,Eden,J.S.,Eden,J.-S." - }, - "country": { - "value": "Australia" - }, - "region": { - "value": "Oceania" - }, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -54662,21 +54857,113 @@ "branch_attrs": { "mutations": { "nuc": [ - "A4687-", - "C4688-", - "A4689-", - "A4690-", - "A4691-" + "C549T", + "T843C", + "G1109A", + "C1694T", + "C2933T", + "T5868C", + "T5880C", + "T6070C", + "T6557C", + "G6573A", + "C6739T", + "G6754A", + "T6887C", + "A7055G", + "G8767A", + "T9029C", + "C10110T", + "A10511T", + "A11306G", + "G11849A", + "G12522A", + "G12698A" + ], + "G": [ + "L104P", + "R165W", + "A170T", + "V214A" + ], + "L": [ + "S534N", + "D1786N" + ], + "N": [ + "S357N" ] + }, + "labels": { + "aa": "G: L104P, R165W, A170T, V214A; L: S534N, D1786N; N: S357N" } - } + }, + "children": [ + { + "name": "MZ851794", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G1928A", + "A2036G", + "C6498T", + "C6629T", + "A9407G", + "G9854A", + "A10322G", + "T12864C" + ], + "G": [ + "S128F" + ], + "L": [ + "S1900P" + ] + }, + "labels": { + "aa": "G: S128F; L: S1900P" + } + } + }, + { + "name": "MZ851793", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A3932G", + "A7418G", + "A7529G", + "T7673C" + ], + "F": [ + "E294G" + ] + }, + "labels": { + "aa": "F: E294G" + } + } + } + ] } ] }, { - "name": "NODE_0000445", + "name": "NODE_0000448", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -54684,44 +54971,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "G36A", - "G954A", - "G1304A", - "A1334G", - "T2311C", - "A2815C", - "G2944A", - "C2962T", - "C3621T", - "C5135T", - "C6000T", - "T6172C", - "C6558T", - "C6887T", - "C7006T", - "A7020C", - "A7481G", - "C8309T", - "G8903A", - "A9020G", - "G9794A", - "T11282C", - "G11951A", - "A13209G" - ], - "G": [ - "A214V" + "G315A" ] - }, - "labels": { - "aa": "G: A214V" } }, "children": [ { - "name": "NODE_0000446", + "name": "NODE_0000449", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -54729,13 +54987,21 @@ "branch_attrs": { "mutations": { "nuc": [ - "A5054G" + "G6886A", + "T7025C", + "T7037C" + ], + "G": [ + "V214I" ] + }, + "labels": { + "aa": "G: V214I" } }, "children": [ { - "name": "OP345084", + "name": "OP358287", "node_attrs": { "div": 0.154, "clade_membership": { @@ -54745,54 +55011,45 @@ "branch_attrs": { "mutations": { "nuc": [ - "C903T", - "T2338C", - "C3735T", - "A3938G", - "T4539C", - "T5174C", - "C5754T", - "G5817A", - "C6012T", - "T6246C", - "A6445T", - "G6610T", - "G6766A", - "A7164G", - "G7370A", - "C8304T", - "C9206T", - "A9410G", - "A9713G", - "A9893G", - "T9923C", - "G10350A", - "A10502G", - "C10514T", - "A11462G", - "A11942G" - ], - "F": [ - "K296R" + "C1186T", + "C1433A", + "T1749C", + "A3036T", + "G3894A", + "C4179T", + "G4632A", + "A6027T", + "G6250A", + "C6454A", + "T6940C", + "A7958G", + "A8074G", + "A8786G", + "A8825G", + "T9474C", + "C10207A", + "C11381T", + "G13239A" ], "G": [ - "S67C", - "D122Y", - "A174T" + "E2K", + "P70T" ], "L": [ - "M68I", - "V1062I", - "I1112M" + "D303G", + "P1014Q" + ], + "P": [ + "S168P" ] }, "labels": { - "aa": "F: K296R; G: S67C, D122Y, A174T; L: M68I, V1062I, I1112M" + "aa": "G: E2K, P70T; L: D303G, P1014Q; P: S168P" } } }, { - "name": "NODE_0000447", + "name": "MN745084", "node_attrs": { "div": 0.154, "clade_membership": { @@ -54802,113 +55059,36 @@ "branch_attrs": { "mutations": { "nuc": [ - "C549T", - "T843C", - "G1109A", - "C1694T", - "C2933T", - "T5868C", - "T5880C", - "T6070C", - "T6557C", - "G6573A", - "C6739T", - "G6754A", - "T6887C", - "A7055G", - "G8767A", - "T9029C", - "C10110T", - "A10511T", - "A11306G", - "G11849A", - "G12522A", - "G12698A" - ], - "G": [ - "L104P", - "R165W", - "A170T", - "V214A" + "A3088G", + "A3332G", + "A3476C", + "A3613T", + "A3614T", + "C6898T", + "C8427T", + "A10247G" ], - "L": [ - "S534N", - "D1786N" + "F": [ + "I13V", + "Q94R", + "K142T", + "K188L" ], - "N": [ - "S357N" + "G": [ + "Q218*" ] }, "labels": { - "aa": "G: L104P, R165W, A170T, V214A; L: S534N, D1786N; N: S357N" - } - }, - "children": [ - { - "name": "MZ851794", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G1928A", - "A2036G", - "C6498T", - "C6629T", - "A9407G", - "G9854A", - "A10322G", - "T12864C" - ], - "G": [ - "S128F" - ], - "L": [ - "S1900P" - ] - }, - "labels": { - "aa": "G: S128F; L: S1900P" - } - } - }, - { - "name": "MZ851793", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A3932G", - "A7418G", - "A7529G", - "T7673C" - ], - "F": [ - "E294G" - ] - }, - "labels": { - "aa": "F: E294G" - } - } + "aa": "F: I13V, Q94R, K142T, K188L; G: Q218*" } - ] + } } ] }, { - "name": "NODE_0000448", + "name": "NODE_0000450", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -54916,13 +55096,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "G315A" + "G6798A", + "C7217T", + "C11741T" ] } }, "children": [ { - "name": "NODE_0000449", + "name": "NODE_0000451", "node_attrs": { "div": 0.153, "clade_membership": { @@ -54932,21 +55114,17 @@ "branch_attrs": { "mutations": { "nuc": [ - "G6886A", - "T7025C", - "T7037C" - ], - "G": [ - "V214I" + "G5682A", + "A7691T", + "T11153C", + "A11387G", + "G12977A" ] - }, - "labels": { - "aa": "G: V214I" } }, "children": [ { - "name": "OP358287", + "name": "MK087726", "node_attrs": { "div": 0.154, "clade_membership": { @@ -54956,47 +55134,19 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1186T", - "C1433A", - "T1749C", - "A3036T", - "G3894A", - "C4179T", - "G4632A", - "A6027T", - "G6250A", - "C6454A", - "T6940C", - "A7958G", - "A8074G", - "A8786G", - "A8825G", - "T9474C", - "C10207A", - "C11381T", - "G13239A" - ], - "G": [ - "E2K", - "P70T" - ], - "L": [ - "D303G", - "P1014Q" - ], - "P": [ - "S168P" + "A3942G", + "A6120C", + "G6121A", + "G6870A", + "A12614C" ] - }, - "labels": { - "aa": "G: E2K, P70T; L: D303G, P1014Q; P: S168P" } } }, { - "name": "MN745084", + "name": "NODE_0000452", "node_attrs": { - "div": 0.153, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55004,34 +55154,94 @@ "branch_attrs": { "mutations": { "nuc": [ - "A3088G", - "A3332G", - "A3476C", - "A3613T", - "A3614T", - "C6898T", - "C8427T", - "A10247G" - ], - "F": [ - "I13V", - "Q94R", - "K142T", - "K188L" + "A1461G", + "T1815C", + "G1892A", + "C2148-", + "G2323A", + "G2981T", + "G3207A", + "C4919T", + "T5574C", + "C5738A", + "T6736C", + "G6808A", + "A6987C", + "G8513A", + "C12077T", + "T12456C" ], "G": [ - "Q218*" + "S164P", + "A188T" + ], + "P": [ + "T72A" + ], + "SH": [ + "T82N" ] }, "labels": { - "aa": "F: I13V, Q94R, K142T, K188L; G: Q218*" + "aa": "G: S164P, A188T; P: T72A; SH: T82N" } - } + }, + "children": [ + { + "name": "OP904028", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A485G", + "T6078C", + "A6208C", + "A6546T", + "G12836A" + ], + "G": [ + "E100D" + ], + "N": [ + "N149S" + ] + }, + "labels": { + "aa": "G: E100D; N: N149S" + } + } + }, + { + "name": "OP904022", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T337C", + "C3247T", + "C3283T", + "C5028T", + "A7163G" + ] + } + } + } + ] } ] }, { - "name": "NODE_0000450", + "name": "NODE_0000453", "node_attrs": { "div": 0.153, "clade_membership": { @@ -55041,15 +55251,72 @@ "branch_attrs": { "mutations": { "nuc": [ - "G6798A", - "C7217T", - "C11741T" + "G6125T", + "A9356G", + "C9470T" ] } }, "children": [ { - "name": "NODE_0000451", + "name": "PP947687", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A243G", + "A918G", + "C996T", + "C1600T", + "A1853T", + "G2278A", + "T2943C", + "C3483T", + "G4260A", + "T4404C", + "T4623C", + "C6438T", + "G6634A", + "G6695A", + "T6887C", + "T6940C", + "T6978C", + "T6996C", + "T6999C", + "T7053C", + "T7089C", + "T7090C", + "T7091C", + "T7098C", + "T7535C", + "C9179T", + "T9245C", + "T10577C", + "T10694G", + "T11153C", + "G11696A", + "T12918C" + ], + "G": [ + "V130I", + "V214A" + ], + "P": [ + "P118L" + ] + }, + "labels": { + "aa": "G: V130I, V214A; P: P118L" + } + } + }, + { + "name": "NODE_0000454", "node_attrs": { "div": 0.153, "clade_membership": { @@ -55057,39 +55324,11 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "G5682A", - "A7691T", - "T11153C", - "A11387G", - "G12977A" - ] - } + "mutations": {} }, "children": [ { - "name": "MK087726", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A3942G", - "A6120C", - "G6121A", - "G6870A", - "A12614C" - ] - } - } - }, - { - "name": "NODE_0000452", + "name": "NODE_0000455", "node_attrs": { "div": 0.154, "clade_membership": { @@ -55099,43 +55338,25 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1461G", - "T1815C", - "G1892A", - "C2148-", - "G2323A", - "G2981T", - "G3207A", - "C4919T", - "T5574C", - "C5738A", - "T6736C", - "G6808A", - "A6987C", - "G8513A", - "C12077T", - "T12456C" - ], - "G": [ - "S164P", - "A188T" - ], - "P": [ - "T72A" + "C1038T", + "G5388A", + "C5454T", + "G5918A", + "C7385T" ], "SH": [ - "T82N" + "R142K" ] }, "labels": { - "aa": "G: S164P, A188T; P: T72A; SH: T82N" + "aa": "SH: R142K" } }, "children": [ { - "name": "OP904028", + "name": "OP345081", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55143,139 +55364,50 @@ "branch_attrs": { "mutations": { "nuc": [ - "A485G", - "T6078C", - "A6208C", - "A6546T", - "G12836A" + "G1383A", + "T1511C", + "T1520C", + "T1562C", + "C2002T", + "C2021T", + "A2190G", + "A3933G", + "G4377A", + "G4512A", + "G5328A", + "G6568A", + "G7427A", + "A8219G", + "C8318T", + "G8336A", + "A8793G", + "A9368T", + "A9710G", + "T11393C" ], "G": [ - "E100D" + "A108T" ], - "N": [ - "N149S" + "L": [ + "N543D" + ], + "M": [ + "Y9C" + ], + "P": [ + "V46I", + "T252I" ] }, "labels": { - "aa": "G: E100D; N: N149S" - } - } - }, - { - "name": "OP904022", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T337C", - "C3247T", - "C3283T", - "C5028T", - "A7163G" - ] + "aa": "G: A108T; L: N543D; M: Y9C; P: V46I, T252I" } } - } - ] - } - ] - }, - { - "name": "NODE_0000453", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G6125T", - "A9356G", - "C9470T" - ] - } - }, - "children": [ - { - "name": "PP947687", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A243G", - "A918G", - "C996T", - "C1600T", - "A1853T", - "G2278A", - "T2943C", - "C3483T", - "G4260A", - "T4404C", - "T4623C", - "C6438T", - "G6634A", - "G6695A", - "T6887C", - "T6940C", - "T6978C", - "T6996C", - "T6999C", - "T7053C", - "T7089C", - "T7090C", - "T7091C", - "T7098C", - "T7535C", - "C9179T", - "T9245C", - "T10577C", - "T10694G", - "T11153C", - "G11696A", - "T12918C" - ], - "G": [ - "V130I", - "V214A" - ], - "P": [ - "P118L" - ] }, - "labels": { - "aa": "G: V130I, V214A; P: P118L" - } - } - }, - { - "name": "NODE_0000454", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - }, - "children": [ { - "name": "NODE_0000455", + "name": "NODE_0000456", "node_attrs": { - "div": 0.153, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55283,23 +55415,38 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1038T", - "G5388A", - "C5454T", - "G5918A", - "C7385T" + "C1200T", + "A1364T", + "A1493G", + "C2148-", + "T2203C", + "T2215C", + "G3480A", + "G5936A", + "G6075A", + "A6150T", + "C6656T", + "T7706C", + "A9716G", + "G10629A" + ], + "G": [ + "P137L" + ], + "L": [ + "V1155I" ], "SH": [ - "R142K" + "R148K" ] }, "labels": { - "aa": "SH: R142K" + "aa": "G: P137L; L: V1155I; SH: R148K" } }, "children": [ { - "name": "OP345081", + "name": "OP904015", "node_attrs": { "div": 0.155, "clade_membership": { @@ -55309,50 +55456,26 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1383A", - "T1511C", - "T1520C", - "T1562C", - "C2002T", - "C2021T", - "A2190G", - "A3933G", - "G4377A", - "G4512A", - "G5328A", - "G6568A", - "G7427A", - "A8219G", - "C8318T", - "G8336A", - "A8793G", - "A9368T", - "A9710G", - "T11393C" - ], - "G": [ - "A108T" + "C7213T", + "C10045T", + "G10661A", + "C12025T" ], "L": [ - "N543D" - ], - "M": [ - "Y9C" - ], - "P": [ - "V46I", - "T252I" + "S16L", + "T960I", + "T1620I" ] }, "labels": { - "aa": "G: A108T; L: N543D; M: Y9C; P: V46I, T252I" + "aa": "L: S16L, T960I, T1620I" } } }, { - "name": "NODE_0000456", + "name": "NODE_0000457", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55360,40 +55483,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1200T", - "A1364T", - "A1493G", - "C2148-", - "T2203C", - "T2215C", - "G3480A", - "G5936A", - "G6075A", - "A6150T", - "C6656T", - "T7706C", - "A9716G", - "G10629A" - ], - "G": [ - "P137L" - ], - "L": [ - "V1155I" - ], - "SH": [ - "R148K" + "A5943G" ] - }, - "labels": { - "aa": "G: P137L; L: V1155I; SH: R148K" } }, "children": [ { - "name": "OP904015", + "name": "OP904027", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55401,26 +55499,30 @@ "branch_attrs": { "mutations": { "nuc": [ - "C7213T", - "C10045T", - "G10661A", - "C12025T" + "T1555C", + "T4958C", + "A11966T", + "A12374G" + ], + "G": [ + "S155N" ], "L": [ - "S16L", - "T960I", - "T1620I" + "I1736M" + ], + "P": [ + "L103P" ] }, "labels": { - "aa": "L: S16L, T960I, T1620I" + "aa": "G: S155N; L: I1736M; P: L103P" } } }, { - "name": "NODE_0000457", + "name": "NODE_0000458", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55428,15 +55530,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "A5943G" + "A6059G" ] } }, "children": [ { - "name": "OP904027", + "name": "OP904152", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55444,30 +55546,18 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1555C", - "T4958C", - "A11966T", - "A12374G" - ], - "G": [ - "S155N" - ], - "L": [ - "I1736M" - ], - "P": [ - "L103P" + "A3777G", + "A7721T", + "C10430T", + "C11588T" ] - }, - "labels": { - "aa": "G: S155N; L: I1736M; P: L103P" } } }, { - "name": "NODE_0000458", + "name": "OP904025", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55475,56 +55565,45 @@ "branch_attrs": { "mutations": { "nuc": [ - "A6059G" + "T9653C" ] } - }, - "children": [ - { - "name": "OP904152", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A3777G", - "A7721T", - "C10430T", - "C11588T" - ] - } - } - }, - { - "name": "OP904025", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T9653C" - ] - } - } - } - ] + } } ] } ] } ] + } + ] + }, + { + "name": "NODE_0000459", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C2148-", + "T9593A", + "G9859A" + ], + "L": [ + "R898K" + ] }, + "labels": { + "aa": "L: R898K" + } + }, + "children": [ { - "name": "NODE_0000459", + "name": "NODE_0000460", "node_attrs": { "div": 0.153, "clade_membership": { @@ -55532,37 +55611,86 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C2148-", - "T9593A", - "G9859A" - ], - "L": [ - "R898K" - ] - }, - "labels": { - "aa": "L: R898K" - } + "mutations": {} }, "children": [ { - "name": "NODE_0000460", + "name": "OP904156", "node_attrs": { - "div": 0.153, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "G316A", + "A1128G", + "G1592A", + "C1612A", + "A2940G", + "A3519T", + "A4071G", + "A4841G", + "T7006C", + "A8136T", + "C9017T", + "A9449G", + "T9711C", + "T13053C" + ], + "L": [ + "N324Y" + ], + "N": [ + "V93I" + ], + "P": [ + "T122N" + ] + }, + "labels": { + "aa": "L: N324Y; N: V93I; P: T122N" + } + } + }, + { + "name": "NODE_0000461", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T201C", + "T774C", + "C1610T", + "C2287A", + "C5409T", + "C5733T", + "C6625T", + "A6859G", + "C6975T", + "A8273C", + "G8654A" + ], + "G": [ + "T205A" + ] + }, + "labels": { + "aa": "G: T205A" + } }, "children": [ { - "name": "OP904156", + "name": "OP904113", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55570,38 +55698,22 @@ "branch_attrs": { "mutations": { "nuc": [ - "G316A", - "A1128G", - "G1592A", - "C1612A", - "A2940G", - "A3519T", - "A4071G", - "A4841G", - "T7006C", - "A8136T", - "C9017T", - "A9449G", - "T9711C", - "T13053C" - ], - "L": [ - "N324Y" + "G2981A", + "T5965C", + "A9281G", + "C11279T" ], - "N": [ - "V93I" - ], - "P": [ - "T122N" + "SH": [ + "Y158H" ] }, "labels": { - "aa": "L: N324Y; N: V93I; P: T122N" + "aa": "SH: Y158H" } } }, { - "name": "NODE_0000461", + "name": "NODE_0000462", "node_attrs": { "div": 0.154, "clade_membership": { @@ -55611,29 +55723,19 @@ "branch_attrs": { "mutations": { "nuc": [ - "T201C", - "T774C", - "C1610T", - "C2287A", - "C5409T", - "C5733T", - "C6625T", - "A6859G", - "C6975T", - "A8273C", - "G8654A" + "A6367G" ], "G": [ - "T205A" + "M41V" ] }, "labels": { - "aa": "G: T205A" + "aa": "G: M41V" } }, "children": [ { - "name": "OP904113", + "name": "OP904121", "node_attrs": { "div": 0.154, "clade_membership": { @@ -55641,26 +55743,13 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "G2981A", - "T5965C", - "A9281G", - "C11279T" - ], - "SH": [ - "Y158H" - ] - }, - "labels": { - "aa": "SH: Y158H" - } + "mutations": {} } }, { - "name": "NODE_0000462", + "name": "NODE_0000463", "node_attrs": { - "div": 0.154, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -55668,21 +55757,45 @@ "branch_attrs": { "mutations": { "nuc": [ - "A6367G" + "T1388C", + "-2148C", + "T2830C", + "C2941A", + "T3705C", + "T3706C", + "G4254A", + "G5391A", + "G5800A", + "A6191G", + "G6968A", + "C8115T", + "C9059T", + "C9119T", + "A9305T", + "C10205T", + "A10484T", + "G11777A", + "G11948A", + "T11957C", + "G12131A", + "G13185A" ], - "G": [ - "M41V" + "L": [ + "H317Y" + ], + "SH": [ + "D103N" ] }, "labels": { - "aa": "G: M41V" + "aa": "L: H317Y; SH: D103N" } }, "children": [ { - "name": "OP904121", + "name": "OY757629", "node_attrs": { - "div": 0.154, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -55692,99 +55805,69 @@ } }, { - "name": "NODE_0000463", + "name": "OY757613", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T1388C", - "-2148C", - "T2830C", - "C2941A", - "T3705C", - "T3706C", - "G4254A", - "G5391A", - "G5800A", - "A6191G", - "G6968A", - "C8115T", - "C9059T", - "C9119T", - "A9305T", - "C10205T", - "A10484T", - "G11777A", - "G11948A", - "T11957C", - "G12131A", - "G13185A" - ], - "L": [ - "H317Y" - ], - "SH": [ - "D103N" - ] - }, - "labels": { - "aa": "L: H317Y; SH: D103N" - } - }, - "children": [ - { - "name": "OY757613", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "OY757629", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + "mutations": {} + } } ] } ] } ] - }, + } + ] + }, + { + "name": "NODE_0000464", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ { - "name": "NODE_0000464", + "name": "NODE_0000465", "node_attrs": { - "div": 0.153, + "div": 0.154, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "C6550T", + "A6895G", + "C10904T" + ], + "G": [ + "P102S", + "M217-", + "Q218-", + "K219-", + "*220-" + ] + }, + "labels": { + "aa": "G: P102S, M217-, Q218-, K219-, *220-" + } }, "children": [ { - "name": "NODE_0000465", + "name": "OP904179", "node_attrs": { - "div": 0.153, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -55792,118 +55875,154 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6550T", - "A6895G", - "C10904T" + "A96G", + "C354T", + "C831T", + "G2179A", + "G3528A", + "T5802C", + "T6061C", + "G6574A", + "G6578T", + "T6643C", + "C6836T", + "T6887C", + "T6940C", + "C7619T", + "G7853A", + "T8639C", + "G11063A", + "C11123T", + "C11931A" ], "G": [ - "P102S", - "M217-", - "Q218-", - "K219-", - "*220-" + "V110M", + "S111I", + "S133P", + "A197V", + "V214A" ] }, "labels": { - "aa": "G: P102S, M217-, Q218-, K219-, *220-" + "aa": "G: V110M, S111I, S133P, A197V, V214A" + } + } + }, + { + "name": "OP904012", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" } }, - "children": [ - { - "name": "OP904179", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A96G", - "C354T", - "C831T", - "G2179A", - "G3528A", - "T5802C", - "T6061C", - "G6574A", - "G6578T", - "T6643C", - "C6836T", - "T6887C", - "T6940C", - "C7619T", - "G7853A", - "T8639C", - "G11063A", - "C11123T", - "C11931A" - ], - "G": [ - "V110M", - "S111I", - "S133P", - "A197V", - "V214A" - ] - }, - "labels": { - "aa": "G: V110M, S111I, S133P, A197V, V214A" - } - } + "branch_attrs": { + "mutations": { + "nuc": [ + "C960T", + "A966G", + "C1769T", + "T2151C", + "G2836A", + "C3574A", + "G4095A", + "C4192T", + "A5517T", + "C6012T", + "T6030C", + "C6775A", + "T7091C", + "T7196C", + "T7674A", + "G7694A", + "G10856A", + "G11372A" + ], + "F": [ + "R175S" + ], + "L": [ + "S170T" + ], + "SH": [ + "K8N" + ] }, - { - "name": "OP904012", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C960T", - "A966G", - "C1769T", - "T2151C", - "G2836A", - "C3574A", - "G4095A", - "C4192T", - "A5517T", - "C6012T", - "T6030C", - "C6775A", - "T7091C", - "T7196C", - "T7674A", - "G7694A", - "G10856A", - "G11372A" - ], - "F": [ - "R175S" - ], - "L": [ - "S170T" - ], - "SH": [ - "K8N" - ] - }, - "labels": { - "aa": "F: R175S; L: S170T; SH: K8N" - } - } + "labels": { + "aa": "F: R175S; L: S170T; SH: K8N" } + } + } + ] + }, + { + "name": "NODE_0000466", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C657T", + "C771T", + "C831T", + "-2148C", + "C2242T", + "T2887C", + "C4467T", + "G5009A", + "T5225C", + "C5733T", + "C6438T", + "G6565A", + "T6730C", + "T6807C", + "T6887C", + "T6999C", + "T7028C", + "T7100C", + "C7174T", + "A7640G", + "A8093G", + "G8124A", + "A8354G", + "C8452T", + "T8648A", + "G8996A", + "C10682T", + "C10895T", + "C10949T", + "A11231C", + "C12386T", + "A12557G", + "G12977A", + "T13013A", + "G13025A" + ], + "G": [ + "A107T", + "F162L", + "V214A" + ], + "L": [ + "P3L", + "V320I", + "T429I", + "K1355N" ] }, + "labels": { + "aa": "G: A107T, F162L, V214A; L: P3L, V320I, T429I, K1355N" + } + }, + "children": [ { - "name": "NODE_0000466", + "name": "OP358288", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -55911,61 +56030,38 @@ "branch_attrs": { "mutations": { "nuc": [ - "C657T", - "C771T", - "C831T", - "-2148C", - "C2242T", - "T2887C", - "C4467T", - "G5009A", - "T5225C", - "C5733T", - "C6438T", - "G6565A", - "T6730C", - "T6807C", - "T6887C", - "T6999C", - "T7028C", - "T7100C", - "C7174T", - "A7640G", - "A8093G", - "G8124A", - "A8354G", - "C8452T", - "T8648A", - "G8996A", - "C10682T", - "C10895T", - "C10949T", - "A11231C", - "C12386T", - "A12557G", - "G12977A", - "T13013A", - "G13025A" - ], - "G": [ - "A107T", - "F162L", - "V214A" + "A5385G", + "A7163G", + "A7164G", + "A7166C" ], - "L": [ - "P3L", - "V320I", - "T429I", - "K1355N" + "M2-2": [ + "I46M" ] }, "labels": { - "aa": "G: A107T, F162L, V214A; L: P3L, V320I, T429I, K1355N" + "aa": "M2-2: I46M" + } + } + }, + { + "name": "NODE_0000467", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G9263A" + ] } }, "children": [ { - "name": "OP358288", + "name": "OP345083", "node_attrs": { "div": 0.156, "clade_membership": { @@ -55975,74 +56071,31 @@ "branch_attrs": { "mutations": { "nuc": [ - "A5385G", - "A7163G", - "A7164G", - "A7166C" - ], - "M2-2": [ - "I46M" + "A10247G" ] - }, - "labels": { - "aa": "M2-2: I46M" } } }, { - "name": "NODE_0000467", - "node_attrs": { - "div": 0.156, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G9263A" - ] - } - }, - "children": [ - { - "name": "OP345083", - "node_attrs": { - "div": 0.156, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A10247G" - ] - } - } - }, - { - "name": "MZ851797", - "node_attrs": { - "div": 0.156, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A3738G", - "T3741C", - "C3747T", - "G13260A", - "G13294A", - "C13332T" - ] - } - } + "name": "MZ851797", + "node_attrs": { + "div": 0.157, + "clade_membership": { + "value": "A2b2" } - ] + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A3738G", + "T3741C", + "C3747T", + "G13260A", + "G13294A", + "C13332T" + ] + } + } } ] } @@ -56061,11 +56114,32 @@ ] } ] - }, + } + ] + }, + { + "name": "NODE_0000468", + "node_attrs": { + "div": 0.15, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A2377G", + "T4431G", + "A7131T", + "G7649A" + ] + } + }, + "children": [ { - "name": "NODE_0000468", + "name": "NODE_0000469", "node_attrs": { - "div": 0.15, + "div": 0.151, "clade_membership": { "value": "A2b2" } @@ -56073,16 +56147,35 @@ "branch_attrs": { "mutations": { "nuc": [ - "A2377G", - "T4431G", - "A7131T", - "G7649A" + "A558C", + "T1748C", + "T2093C", + "A3936G", + "G6574A", + "G6835A", + "A7046T", + "G7319A", + "A10278G", + "C10331T", + "A11141G", + "C12713T", + "A13121G" + ], + "G": [ + "V110M", + "A197T" + ], + "L": [ + "N1038D" ] + }, + "labels": { + "aa": "G: V110M, A197T; L: N1038D" } }, "children": [ { - "name": "NODE_0000469", + "name": "NODE_0000470", "node_attrs": { "div": 0.151, "clade_membership": { @@ -56092,37 +56185,74 @@ "branch_attrs": { "mutations": { "nuc": [ - "A558C", - "T1748C", - "T2093C", - "A3936G", - "G6574A", - "G6835A", - "A7046T", - "G7319A", - "A10278G", - "C10331T", - "A11141G", - "C12713T", - "A13121G" - ], - "G": [ - "V110M", - "A197T" - ], - "L": [ - "N1038D" + "T6711C" ] - }, - "labels": { - "aa": "G: V110M, A197T; L: N1038D" } }, "children": [ { - "name": "NODE_0000470", + "name": "OP904083", "node_attrs": { - "div": 0.151, + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A1116G", + "G1550A", + "A1639G", + "C2148-", + "C3028T", + "A3489G", + "C3711T", + "G4416A", + "T4587C", + "C4811T", + "A4937G", + "C4961T", + "T6339C", + "T6344C", + "C6527T", + "C6581T", + "C6632T", + "A6816C", + "A7127G", + "G7438A", + "A7649G", + "T8402C", + "A8501G", + "C8921T", + "C8933T", + "T9758C", + "G9806A", + "T11363C" + ], + "G": [ + "L33S", + "P94L", + "P112L", + "S129F", + "F162L" + ], + "L": [ + "S91N" + ], + "P": [ + "N131S" + ] + }, + "labels": { + "aa": "G: L33S, P94L, P112L, S129F, F162L; L: S91N; P: N131S" + } + } + }, + { + "name": "NODE_0000471", + "node_attrs": { + "div": 0.152, "clade_membership": { "value": "A2b2" } @@ -56130,13 +56260,38 @@ "branch_attrs": { "mutations": { "nuc": [ - "T6711C" + "G876A", + "G2015A", + "T3462C", + "T5081C", + "T5089C", + "C5968T", + "C7078T", + "T7120C", + "G7760A", + "C8381A", + "A8526G", + "A10394G", + "T11027C", + "C12932T" + ], + "L": [ + "I454V" + ], + "M2-1": [ + "L118P" + ], + "SH": [ + "H159Y" ] + }, + "labels": { + "aa": "L: I454V; M2-1: L118P; SH: H159Y" } }, "children": [ { - "name": "OP904083", + "name": "NODE_0000472", "node_attrs": { "div": 0.153, "clade_membership": { @@ -56146,99 +56301,23 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1116G", - "G1550A", - "A1639G", - "C2148-", - "C3028T", - "A3489G", - "C3711T", - "G4416A", - "T4587C", - "C4811T", - "A4937G", - "C4961T", - "T6339C", - "T6344C", - "C6527T", - "C6581T", - "C6632T", - "A6816C", - "A7127G", - "G7438A", - "A7649G", - "T8402C", - "A8501G", - "C8921T", - "C8933T", - "T9758C", - "G9806A", - "T11363C" - ], - "G": [ - "L33S", - "P94L", - "P112L", - "S129F", - "F162L" - ], - "L": [ - "S91N" - ], - "P": [ - "N131S" - ] - }, - "labels": { - "aa": "G: L33S, P94L, P112L, S129F, F162L; L: S91N; P: N131S" - } - } - }, - { - "name": "NODE_0000471", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G876A", - "G2015A", - "T3462C", - "T5081C", - "T5089C", - "C5968T", - "C7078T", - "T7120C", - "G7760A", - "C8381A", - "A8526G", - "A10394G", - "T11027C", - "C12932T" + "T1122C", + "T6420A", + "C8653A" ], "L": [ - "I454V" - ], - "M2-1": [ - "L118P" - ], - "SH": [ - "H159Y" + "T496K" ] }, "labels": { - "aa": "L: I454V; M2-1: L118P; SH: H159Y" + "aa": "L: T496K" } }, "children": [ { - "name": "NODE_0000472", + "name": "PP947632", "node_attrs": { - "div": 0.152, + "div": 0.157, "clade_membership": { "value": "A2b2" } @@ -56246,23 +56325,142 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1122C", - "T6420A", - "C8653A" + "G51A", + "T336A", + "G492A", + "T577C", + "C1032A", + "C1635T", + "G1661A", + "C2372T", + "T2494C", + "T2617C", + "G2821A", + "A2875G", + "A3174T", + "C3471T", + "G3528A", + "T3627C", + "C3747T", + "C3918T", + "T4227C", + "C4584T", + "G5201A", + "A5215G", + "G5670A", + "C5745T", + "T5928C", + "C6012T", + "T6015C", + "C6068T", + "C6139T", + "A6161G", + "T6167G", + "A6170G", + "T6246C", + "G6274A", + "A6333G", + "C6391T", + "G6757A", + "T6864C", + "A7000G", + "T7131C", + "C7358T", + "A7372G", + "C7775T", + "C7872T", + "A7928G", + "G8513A", + "T8546C", + "G8651A", + "T9740C", + "C10388T", + "C10688T", + "G11141A", + "G11402A", + "C11576A", + "C11999T", + "G12410A", + "C12572T", + "G12818A", + "G12836A", + "C12897T" + ], + "G": [ + "A10T", + "P163S" + ], + "L": [ + "K69R" + ], + "M2-1": [ + "K160R" + ], + "P": [ + "P130S" + ] + }, + "labels": { + "aa": "G: A10T, P163S; L: K69R; M2-1: K160R; P: P130S" + } + } + }, + { + "name": "NODE_0000473", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A426G", + "T474C", + "G2300A", + "A2515G", + "C3283T", + "A3300G", + "T4359C", + "T4407C", + "C4559T", + "A5886G", + "A6182C", + "A6751G", + "C6887T", + "C7697T", + "A10328G", + "G10805A", + "T11552G", + "A11991G", + "T12149C", + "C12861T", + "T13240C" + ], + "F": [ + "S503F" + ], + "G": [ + "K169E", + "A214V" ], "L": [ - "T496K" + "I1609V" + ], + "M": [ + "A46T" ] }, "labels": { - "aa": "L: T496K" + "aa": "F: S503F; G: K169E, A214V; L: I1609V; M: A46T" } }, "children": [ { - "name": "PP947632", + "name": "PP947675", "node_attrs": { - "div": 0.157, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -56270,90 +56468,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "G51A", - "T336A", - "G492A", - "T577C", - "C1032A", - "C1635T", - "G1661A", - "C2372T", - "T2494C", - "T2617C", - "G2821A", - "A2875G", - "A3174T", - "C3471T", - "G3528A", - "T3627C", - "C3747T", - "C3918T", - "T4227C", - "C4584T", - "G5201A", - "A5215G", - "G5670A", - "C5745T", - "T5928C", - "C6012T", - "T6015C", - "C6068T", - "C6139T", - "A6161G", - "T6167G", - "A6170G", - "T6246C", - "G6274A", - "A6333G", - "C6391T", - "G6757A", - "T6864C", - "A7000G", - "T7131C", - "C7358T", - "A7372G", - "C7775T", - "C7872T", - "A7928G", - "G8513A", - "T8546C", - "G8651A", - "T9740C", - "C10388T", - "C10688T", - "G11141A", - "G11402A", - "C11576A", - "C11999T", - "G12410A", - "C12572T", - "G12818A", - "G12836A", - "C12897T" - ], - "G": [ - "A10T", - "P163S" - ], - "L": [ - "K69R" - ], - "M2-1": [ - "K160R" - ], - "P": [ - "P130S" + "G144A" ] - }, - "labels": { - "aa": "G: A10T, P163S; L: K69R; M2-1: K160R; P: P130S" } } }, { - "name": "NODE_0000473", + "name": "NODE_0000474", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -56361,51 +56484,23 @@ "branch_attrs": { "mutations": { "nuc": [ - "A426G", - "T474C", - "G2300A", - "A2515G", - "C3283T", - "A3300G", - "T4359C", - "T4407C", - "C4559T", - "A5886G", - "A6182C", - "A6751G", - "C6887T", - "C7697T", - "A10328G", - "G10805A", - "T11552G", - "A11991G", - "T12149C", - "C12861T", - "T13240C" - ], - "F": [ - "S503F" + "T157C", + "A5424G", + "G6862A" ], "G": [ - "K169E", - "A214V" - ], - "L": [ - "I1609V" - ], - "M": [ - "A46T" + "G206S" ] }, "labels": { - "aa": "F: S503F; G: K169E, A214V; L: I1609V; M: A46T" + "aa": "G: G206S" } }, "children": [ { - "name": "PP947675", + "name": "PP947677", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -56413,113 +56508,172 @@ "branch_attrs": { "mutations": { "nuc": [ - "G144A" + "T6865C", + "T6885C", + "T6887C", + "T7028C", + "A7368G" + ], + "G": [ + "S207P", + "V214A" + ], + "L": [ + "M68V" ] + }, + "labels": { + "aa": "G: S207P, V214A; L: M68V" } } }, { - "name": "NODE_0000474", + "name": "NODE_0000475", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T157C", - "A5424G", - "G6862A" - ], - "G": [ - "G206S" - ] - }, - "labels": { - "aa": "G: G206S" - } + "mutations": {} }, "children": [ { - "name": "PP947677", + "name": "PP947654", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T6865C", - "T6885C", - "T6887C", - "T7028C", - "A7368G" - ], - "G": [ - "S207P", - "V214A" - ], - "L": [ - "M68V" - ] - }, - "labels": { - "aa": "G: S207P, V214A; L: M68V" - } + "mutations": {} } }, { - "name": "NODE_0000475", + "name": "PP947638", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { "mutations": {} - }, - "children": [ - { - "name": "PP947654", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "PP947638", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + } } ] } ] } ] + } + ] + }, + { + "name": "NODE_0000476", + "node_attrs": { + "div": 0.157, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A39G", + "A579G", + "C828T", + "T1083C", + "G1339A", + "C1424T", + "G1483A", + "C2148-", + "A2698G", + "A3339G", + "A3612T", + "G3972A", + "G4095A", + "C4263T", + "T4278C", + "C4540T", + "T4563C", + "T4638C", + "G4748A", + "T4799C", + "C4817T", + "C4964A", + "A5587G", + "A5708G", + "C5820T", + "A5906G", + "A6076T", + "C6138A", + "A6157G", + "A6187G", + "T6231C", + "A6411G", + "T6444C", + "C6550T", + "C6552T", + "A6674G", + "A6681C", + "T6682C", + "C6891A", + "T7013C", + "T7031C", + "G7138A", + "C7217T", + "G7588A", + "C7601T", + "A7676G", + "A8219G", + "C8480T", + "T9617A", + "T9698C", + "A9920G", + "T10172C", + "G10532A", + "C11876T", + "A12390G", + "A12422G", + "G12914A", + "A13205C", + "G13233A", + "A13301C" + ], + "G": [ + "I55M", + "P102S", + "K143R", + "K145N", + "S146P", + "S215R" + ], + "L": [ + "S141N", + "I1742V" + ], + "P": [ + "S31N", + "R79K" + ], + "SH": [ + "I32V", + "D72G", + "N138S" + ] }, + "labels": { + "aa": "G: I55M, P102S, K143R, K145N, S146P, S215R; L: S141N, I1742V; P: S31N, R79K; SH: I32V, D72G, N138S" + } + }, + "children": [ { - "name": "NODE_0000476", + "name": "NODE_0000477", "node_attrs": { - "div": 0.156, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -56527,98 +56681,43 @@ "branch_attrs": { "mutations": { "nuc": [ - "A39G", - "A579G", - "C828T", - "T1083C", - "G1339A", - "C1424T", - "G1483A", - "C2148-", - "A2698G", - "A3339G", - "A3612T", - "G3972A", - "G4095A", - "C4263T", - "T4278C", - "C4540T", - "T4563C", - "T4638C", - "G4748A", - "T4799C", - "C4817T", - "C4964A", - "A5587G", - "A5708G", - "C5820T", - "A5906G", - "A6076T", - "C6138A", - "A6157G", - "A6187G", - "T6231C", - "A6411G", - "T6444C", - "C6550T", - "C6552T", - "A6674G", - "A6681C", - "T6682C", - "C6891A", - "T7013C", - "T7031C", - "G7138A", - "C7217T", - "G7588A", - "C7601T", - "A7676G", - "A8219G", - "C8480T", - "T9617A", - "T9698C", - "A9920G", - "T10172C", - "G10532A", - "C11876T", - "A12390G", - "A12422G", - "G12914A", - "A13205C", - "G13233A", - "A13301C" - ], - "G": [ - "I55M", - "P102S", - "K143R", - "K145N", - "S146P", - "S215R" + "C1020T", + "G1766A", + "C3085T", + "C3585T", + "C4625T", + "T4985A", + "A5083G", + "A5607G", + "G5692A", + "A5819G", + "T6852C", + "C7069T", + "T9203C", + "C9578T", + "C12824T", + "A13151G" ], - "L": [ - "S141N", - "I1742V" + "F": [ + "P525L" ], - "P": [ - "S31N", - "R79K" + "M2-1": [ + "N116S" ], "SH": [ - "I32V", - "D72G", - "N138S" + "E67K", + "D109G" ] }, "labels": { - "aa": "G: I55M, P102S, K143R, K145N, S146P, S215R; L: S141N, I1742V; P: S31N, R79K; SH: I32V, D72G, N138S" + "aa": "F: P525L; M2-1: N116S; SH: E67K, D109G" } }, "children": [ { - "name": "NODE_0000477", + "name": "OP904170", "node_attrs": { - "div": 0.158, + "div": 0.159, "clade_membership": { "value": "A2b2" } @@ -56626,41 +56725,44 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1020T", - "G1766A", - "C3085T", - "C3585T", - "C4625T", - "T4985A", - "A5083G", - "A5607G", - "G5692A", - "A5819G", - "T6852C", - "C7069T", - "T9203C", - "C9578T", - "C12824T", - "A13151G" + "G236T", + "G256A", + "A3501T", + "G3867A", + "G4667A", + "C6327T" ], "F": [ - "P525L" - ], - "M2-1": [ - "N116S" + "S539N" ], - "SH": [ - "E67K", - "D109G" + "N": [ + "G66V", + "A73T" ] }, "labels": { - "aa": "F: P525L; M2-1: N116S; SH: E67K, D109G" + "aa": "F: S539N; N: G66V, A73T" + } + } + }, + { + "name": "NODE_0000478", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G11354A" + ] } }, "children": [ { - "name": "OP904170", + "name": "OP904173", "node_attrs": { "div": 0.158, "clade_membership": { @@ -56670,28 +56772,87 @@ "branch_attrs": { "mutations": { "nuc": [ - "G236T", - "G256A", - "A3501T", - "G3867A", - "G4667A", - "C6327T" + "C423T", + "C6349A" ], - "F": [ - "S539N" + "G": [ + "L35I" + ] + }, + "labels": { + "aa": "G: L35I" + } + } + }, + { + "name": "OP904161", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T154C", + "A10073G" ], "N": [ - "G66V", - "A73T" + "S39P" ] }, "labels": { - "aa": "F: S539N; N: G66V, A73T" + "aa": "N: S39P" } } - }, + } + ] + } + ] + }, + { + "name": "NODE_0000479", + "node_attrs": { + "div": 0.157, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C6887T" + ], + "G": [ + "A214V" + ] + }, + "labels": { + "aa": "G: A214V" + } + }, + "children": [ + { + "name": "NODE_0000480", + "node_attrs": { + "div": 0.157, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C1607T", + "A2908G", + "C4335T" + ] + } + }, + "children": [ { - "name": "NODE_0000478", + "name": "NODE_0000481", "node_attrs": { "div": 0.158, "clade_membership": { @@ -56701,13 +56862,59 @@ "branch_attrs": { "mutations": { "nuc": [ - "G11354A" + "-2148G", + "G5784A", + "A7271G", + "A9791G", + "G10859A" + ] + } + }, + "children": [ + { + "name": "OY757726", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "OY757690", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + } + } + ] + }, + { + "name": "NODE_0000482", + "node_attrs": { + "div": 0.157, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G3438A" ] } }, "children": [ { - "name": "OP904173", + "name": "OP904166", "node_attrs": { "div": 0.158, "clade_membership": { @@ -56717,20 +56924,22 @@ "branch_attrs": { "mutations": { "nuc": [ - "C423T", - "C6349A" + "G5922A", + "G6472A", + "A8579G", + "A9941G" ], "G": [ - "L35I" + "E76K" ] }, "labels": { - "aa": "G: L35I" + "aa": "G: E76K" } } }, { - "name": "OP904161", + "name": "NODE_0000483", "node_attrs": { "div": 0.158, "clade_membership": { @@ -56740,26 +56949,89 @@ "branch_attrs": { "mutations": { "nuc": [ - "T154C", - "A10073G" + "C1582T", + "G6565A", + "G6750A", + "A11604G", + "T11750C" ], - "N": [ - "S39P" + "G": [ + "A107T" + ], + "L": [ + "I1480V" + ], + "P": [ + "A112V" ] }, "labels": { - "aa": "N: S39P" + "aa": "G: A107T; L: I1480V; P: A112V" } - } + }, + "children": [ + { + "name": "OP904174", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A4071G", + "T4074C", + "C4429T", + "C4434G", + "C4435G", + "G4511A", + "T6552C", + "T6730C", + "G9371A" + ], + "F": [ + "D461E", + "Q462E", + "G487E" + ], + "G": [ + "F162L" + ] + }, + "labels": { + "aa": "F: D461E, Q462E, G487E; G: F162L" + } + } + }, + { + "name": "OP904164", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T4053C", + "A10715G" + ] + } + } + } + ] } ] } ] }, { - "name": "NODE_0000479", + "name": "NODE_0000484", "node_attrs": { - "div": 0.156, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -56767,39 +57039,43 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6887T" + "C294T", + "G573T", + "G1892A", + "C3483T", + "A4094G", + "G5388A", + "A6228T", + "A11254G" ], - "G": [ - "A214V" + "F": [ + "K348R" + ], + "L": [ + "K1363R" ] }, "labels": { - "aa": "G: A214V" + "aa": "F: K348R; L: K1363R" } }, "children": [ { - "name": "NODE_0000480", + "name": "NODE_0000485", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C1607T", - "A2908G", - "C4335T" - ] - } + "mutations": {} }, "children": [ { - "name": "NODE_0000481", + "name": "OP904165", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -56807,45 +57083,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "-2148G", - "G5784A", - "A7271G", - "A9791G", - "G10859A" + "C4161T" ] } - }, - "children": [ - { - "name": "OY757726", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "OY757690", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + } }, { - "name": "NODE_0000482", + "name": "NODE_0000486", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -56853,15 +57099,24 @@ "branch_attrs": { "mutations": { "nuc": [ - "G3438A" + "T6441C", + "T6477C", + "T6626C", + "T6864C" + ], + "G": [ + "L127P" ] + }, + "labels": { + "aa": "G: L127P" } }, "children": [ { - "name": "OP904166", + "name": "OP904168", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -56869,114 +57124,47 @@ "branch_attrs": { "mutations": { "nuc": [ - "G5922A", - "G6472A", - "A8579G", - "A9941G" + "G915A", + "C1032T", + "G1851A" ], - "G": [ - "E76K" + "P": [ + "A202T" ] }, "labels": { - "aa": "G: E76K" + "aa": "P: A202T" } } - }, - { - "name": "NODE_0000483", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1582T", - "G6565A", - "G6750A", - "A11604G", - "T11750C" - ], - "G": [ - "A107T" - ], - "L": [ - "I1480V" - ], - "P": [ - "A112V" - ] - }, - "labels": { - "aa": "G: A107T; L: I1480V; P: A112V" + }, + { + "name": "OP904163", + "node_attrs": { + "div": 0.158, + "clade_membership": { + "value": "A2b2" } }, - "children": [ - { - "name": "OP904174", - "node_attrs": { - "div": 0.158, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A4071G", - "T4074C", - "C4429T", - "C4434G", - "C4435G", - "G4511A", - "T6552C", - "T6730C", - "G9371A" - ], - "F": [ - "D461E", - "Q462E", - "G487E" - ], - "G": [ - "F162L" - ] - }, - "labels": { - "aa": "F: D461E, Q462E, G487E; G: F162L" - } - } - }, - { - "name": "OP904164", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T4053C", - "A10715G" - ] - } - } + "branch_attrs": { + "mutations": { + "nuc": [ + "A3351G", + "C3471T", + "T7547C", + "T7562G", + "C9765T" + ] } - ] + } } ] } ] }, { - "name": "NODE_0000484", + "name": "NODE_0000487", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -56984,31 +57172,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C294T", - "G573T", - "G1892A", - "C3483T", - "A4094G", - "G5388A", - "A6228T", - "A11254G" - ], - "F": [ - "K348R" - ], - "L": [ - "K1363R" + "T4281C" ] - }, - "labels": { - "aa": "F: K348R; L: K1363R" } }, "children": [ { - "name": "NODE_0000485", + "name": "NODE_0000488", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -57018,164 +57190,80 @@ }, "children": [ { - "name": "OP904165", + "name": "OP904172", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C4161T" - ] - } + "mutations": {} } }, { - "name": "NODE_0000486", + "name": "OP904162", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T6441C", - "T6477C", - "T6626C", - "T6864C" - ], - "G": [ - "L127P" - ] - }, - "labels": { - "aa": "G: L127P" - } - }, - "children": [ - { - "name": "OP904168", - "node_attrs": { - "div": 0.158, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G915A", - "C1032T", - "G1851A" - ], - "P": [ - "A202T" - ] - }, - "labels": { - "aa": "P: A202T" - } - } - }, - { - "name": "OP904163", - "node_attrs": { - "div": 0.158, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A3351G", - "C3471T", - "T7547C", - "T7562G", - "C9765T" - ] - } - } - } - ] + "mutations": {} + } } ] }, { - "name": "NODE_0000487", + "name": "NODE_0000489", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T4281C" - ] - } + "mutations": {} }, "children": [ { - "name": "NODE_0000488", + "name": "OP904167", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "OP904172", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "OP904162", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } + "mutations": { + "nuc": [ + "T11075C" + ] } - ] + } }, { - "name": "NODE_0000489", + "name": "NODE_0000490", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "G1304A", + "C11724T" + ] + } }, "children": [ { - "name": "OP904167", + "name": "OP904171", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -57183,64 +57271,29 @@ "branch_attrs": { "mutations": { "nuc": [ - "T11075C" + "A10644G", + "A10808G" + ], + "L": [ + "S1160G" ] + }, + "labels": { + "aa": "L: S1160G" } } }, { - "name": "NODE_0000490", + "name": "OP904169", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "G1304A", - "C11724T" - ] - } - }, - "children": [ - { - "name": "OP904171", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A10644G", - "A10808G" - ], - "L": [ - "S1160G" - ] - }, - "labels": { - "aa": "L: S1160G" - } - } - }, - { - "name": "OP904169", - "node_attrs": { - "div": 0.157, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + "mutations": {} + } } ] } @@ -57255,23 +57308,123 @@ ] } ] - }, + } + ] + }, + { + "name": "NODE_0000491", + "node_attrs": { + "div": 0.151, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ { - "name": "NODE_0000491", + "name": "NODE_0000492", "node_attrs": { - "div": 0.151, + "div": 0.152, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "G177A", + "G315A", + "T6950C" + ] + } }, "children": [ { - "name": "NODE_0000492", + "name": "PP947646", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G117A", + "A132G", + "T766C", + "A1029T", + "C1203T", + "A1927G", + "C2392A", + "A3588G", + "A3687G", + "G3894A", + "G3939A", + "T4047C", + "T4053C", + "T4074C", + "G4605A", + "A4829G", + "C5021T", + "G5201A", + "A5821G", + "C5907T", + "C5916T", + "C6055A", + "T6112-", + "T6113-", + "G6715T", + "A6765G", + "C6789T", + "C6825T", + "T6864A", + "A7071G", + "C7114T", + "A7621G", + "C7964T", + "T8225C", + "T8570A", + "T9156C", + "A9911T", + 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"A10178T", + "A10286G", + "G10676A", + "C11087T", + "G11285T", + "C11588T", + "C11837T", + "A12200G", + "G12515A", + "A12866T" + ], + "G": [ + "M110T", + "A170T" + ], + "N": [ + "K107R" + ], + "SH": [ + "F44L", + "D87N", + "P132S", + "I178T" ] + }, + "labels": { + "aa": "G: M110T, A170T; N: K107R; SH: F44L, D87N, P132S, I178T" } }, "children": [ { - "name": "PP947646", + "name": "PP947648", "node_attrs": { - "div": 0.154, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -57297,79 +57507,35 @@ "branch_attrs": { "mutations": { "nuc": [ - "G117A", - "A132G", - "T766C", - "A1029T", - "C1203T", - "A1927G", - "C2392A", - "A3588G", - "A3687G", - "G3894A", - "G3939A", - "T4047C", - "T4053C", - "T4074C", - "G4605A", - "A4829G", - "C5021T", - "G5201A", - "A5821G", - "C5907T", - "C5916T", - "C6055A", - "T6112-", - "T6113-", - "G6715T", - "A6765G", - "C6789T", - "C6825T", - "T6864A", - "A7071G", - "C7114T", - "A7621G", - "C7964T", - "T8225C", - "T8570A", - "T9156C", - "A9911T", - 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+ } + }, + "children": [ + { + "name": "NODE_0000495", + "node_attrs": { + "div": 0.152, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A2299G", + "A2431G", + "A2936C", + "C3621T", + "C4107A", + "A8735G" + ] + } + }, + "children": [ + { + "name": "NODE_0000496", + "node_attrs": { + "div": 0.152, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G2091A", + "T2830C", + "T2954C", + "G5694A" ], - "SH": [ - "F44L", - "D87N", - "P132S", - "I178T" + "P": [ + "D282N" ] }, "labels": { - "aa": "G: M110T, A170T; N: K107R; SH: F44L, D87N, P132S, I178T" + "aa": "P: D282N" } }, "children": [ { - "name": "PP947648", + "name": "OP904134", "node_attrs": { - "div": 0.155, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -57452,33 +57664,232 @@ "branch_attrs": { "mutations": { "nuc": [ - "G65A", - "T2590C", - "T3951C", - "C5265T", - "C5550A", - "C6499T", - "C6887T", - "A7400T", - 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"mutations": { + "nuc": [ + "G270A", + "C657T", + "A1307G", + "T1395C", + "T1406C", + "G1496A", + "T1709A", + "T1725C", + "A2976G", + "A3729G", + "G3894A", + "T4158C", + "G4549A", + "T5802C", + "T5903C", + "C6016T", + "T6441C", + "T6495C", + "C6564T", + "A6574G", + "G6578A", + "T6864C", + "C8304T", + "A8321T", + "G8393A", + "C8564T", + "A8615G", + "T8681C", + "G9722A", + "T10094C", + "A10367T", + "C10772T", + "G11669A", + "G12128A" + ], + "F": [ + "V500I" + ], + "G": [ + "M110V", + "S111N" + ], + "P": [ + "D154E" + ], + "SH": [ + "I137T", + "H175Y" + ] + }, + "labels": { + "aa": "F: V500I; G: M110V, S111N; P: D154E; SH: I137T, H175Y" + } + } + }, + { + "name": "MZ851796", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C1131T", + "T1555C", + "G2018A", + "A2698G", + "T2965C", + "A3330G", + "C4335T", + "G4377A", + "T4468C", + "C4811T", + "T5786C", + "G5926A", + "A6466T", + "T6633C", + "T6711C", + "G7137A", + "A7164G", + "C7775T", + "G8011A", + "A9484G", + "T11179C", + "G13199A", + "T13240C" + ], + "G": [ + "N74Y" + ], + "L": [ + "R282K", + "K773R", + "I1338T" + ], + "P": [ + "L103P" + ], + "SH": [ + "I98T", + "D145N" + ] + }, + "labels": { + "aa": "G: N74Y; L: R282K, K773R, I1338T; P: L103P; SH: I98T, D145N" + } + } + } + ] + } + ] + }, + { + "name": "NODE_0000498", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T336A", + "C942A", + "A1850G", + "T2896C", + "C2930T", + "C2942T", + "G3513A", + "C4925T", + "A5352G", + "G7370A", + "G8903A", + "C12962T" + ], + "L": [ + "M68I" + ] + }, + "labels": { + "aa": "L: M68I" + } + }, + "children": [ + { + "name": "PP947676", "node_attrs": { "div": 0.156, "clade_membership": { @@ -57488,56 +57899,256 @@ "branch_attrs": { "mutations": { "nuc": [ - "T577C", - "C1017A", - "T1122C", - "G1205A", - "G1376A", - "T2314C", - "G2914A", - "T3447C", - "C3531T", - "C4601T", - "A5616G", - "C6351T", - "T6631C", - "T6711C", - "C7088T", - "C7733T", - "G8124A", - "T8682C", - "C10011T", - "C10061T", - "A11684G", - "G12908A" - ], - "F": [ - "T517I" - ], - "G": [ - "S129P" + "C209T", + "G264A", + "C675A", + "G816A", + "A861T", + "G1339A", + "G2180A", + "C2258T", + "G2614A", + "C2936A", + "C3006A", + "A3357G", + "T3453C", + "T3624C", + "T3705C", + "T4563C", + "T4587C", + "C4919T", + "G4970A", + "C5696T", + "G5793A", + "C5820T", + "G5837T", + "C5951T", + "T6131A", + "C6402T", + "T6864C", + "A7081T", + "A7184G", + "G7488A", + "G8118T", + "T8210C", + "G8692A", + "A8778G", + "T9176C", + "C9629T", + "T10490A", + "G11192A", + "T11204C", + "C12755T", + "C12965T" ], "L": [ - "V320I", - "F506L" + "G108S", + "G318C", + "S509N", + "R538G" + ], + "M": [ + "V6I", + "M150I" ], "N": [ - "S389N" + "T57I", + "D212E" + ], + "P": [ + "S31N" + ], + "SH": [ + "P68L", + "S115I", + "P153L" + ] + }, + "labels": { + "aa": "L: G108S, G318C, S509N, R538G; M: V6I, M150I; N: T57I, D212E; P: S31N; SH: P68L, S115I, P153L" + } + } + }, + { + "name": "NODE_0000499", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A6674G", + "G13082A" + ], + "G": [ + "I153T", + "F162L" + ] + }, + "labels": { + "aa": "G: I153T, F162L" + } + }, + "children": [ + { + "name": "PP947607", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T91C", + "C1017A", + "C1134T", + "G1664A", + "T1994C", + "T2086G", + "C2318T", + "C2563T", + "G3150A", + "G3278A", + "T3405A", + "C3747T", + "T4742A", + "C6552T", + "C6850T", + "C7217T", + "T7517G", + "T7527C", + "C7982T", + "T8519A", + "A9186G", + "T9863C", + "A10016T", + "A10046G", + "G10091A", + "T11084A", + "G11285A", + "T11307C", + "C12473T", + "G12686A", + "A13203G", + "A13251G" + ], + "F": [ + "S76N" + ], + "G": [ + "H202Y" + ], + "L": [ + "D117E", + "M674V", + "L950F" + ], + "P": [ + "L280R" + ] + }, + "labels": { + "aa": "F: S76N; G: H202Y; L: D117E, M674V, L950F; P: L280R" + } + } + }, + { + "name": "NODE_0000500", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C996T", + "G1476A", + "T1883C", + "G3936A", + "C3958T", + "G5918A", + "T6711C", + "C6802T", + "G6897A", + "A7226T", + "C8726T", + "A8780G", + "C8990T", + "T9671C", + "A10044G", + "G10454A", + "G10488A", + "A11990T", + "C12924A" + ], + "G": [ + "P186S", + "M217I" + ], + "L": [ + "T960A", + "V1108I", + "L1920I" + ], + "P": [ + "A77T" + ], + "SH": [ + "R142K" + ] + }, + "labels": { + "aa": "G: P186S, M217I; L: T960A, V1108I, L1920I; P: A77T; SH: R142K" + } + }, + "children": [ + { + "name": "PP947698", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G2984A" + ] + } + } + }, + { + "name": "PP947669", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + } + } ] - }, - "labels": { - "aa": "F: T517I; G: S129P; L: V320I, F506L; N: S389N" } - } + ] } ] } ] }, { - "name": "NODE_0000494", + "name": "NODE_0000501", "node_attrs": { - "div": 0.151, + "div": 0.152, "clade_membership": { "value": "A2b2" } @@ -57545,17 +58156,21 @@ "branch_attrs": { "mutations": { "nuc": [ - "A396G", - "C2491T", - "C6495T" + "C6887T" + ], + "G": [ + "A214V" ] + }, + "labels": { + "aa": "G: A214V" } }, "children": [ { - "name": "NODE_0000495", + "name": "NODE_0000502", "node_attrs": { - "div": 0.151, + "div": 0.152, "clade_membership": { "value": "A2b2" } @@ -57563,20 +58178,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "A2299G", - "A2431G", - "A2936C", - "C3621T", - "C4107A", - "A8735G" + "T3627C" ] } }, "children": [ { - "name": "NODE_0000496", + "name": "NODE_0000503", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -57584,22 +58194,44 @@ "branch_attrs": { "mutations": { "nuc": [ - "G2091A", - "T2830C", - "T2954C", - "G5694A" + "G346A", + "T1725C", + "A2027G", + "C2148-", + "C3846T", + "T6042C", + "T6153C", + "T6160C", + "T6167C", + "T6168C", + "T6190C", + "T6206C", + "T6213C", + "T6607C", + "C7556T", + "C8240T", + "A8303G", + "G9476A", + "T10051A", + "A10073G" ], - "P": [ - "D282N" + "G": [ + "S121P" + ], + "L": [ + "I962K" + ], + "N": [ + "V103I" ] }, "labels": { - "aa": "P: D282N" + "aa": "G: S121P; L: I962K; N: V103I" } }, "children": [ { - "name": "OP904134", + "name": "OP904096", "node_attrs": { "div": 0.154, "clade_membership": { @@ -57609,56 +58241,36 @@ "branch_attrs": { "mutations": { "nuc": [ - "T606C", - "C814T", - "C1038T", - "T1625C", - "C2148-", - "C2563A", - "C3294T", - "T5081C", - "A5231G", - "C5970T", - "G6126A", - "G6788A", - "C6834T", - "T6896C", - "G6897A", - "C6898A", - "A6899G", - "A6902T", - "T6904-", - "A6905-", - "G6906-", - "-6926G", - "T6940C", - "T7902C", - "T8027C", - "G8767A", - "T9824C", - "T9836C", - "T10314C", - "T10604A", - "A10976G", - "C12599T", - "C12611T" + "C4233T", + "C4609T", + "G6145A", + "A6470G", + "T6965C", + "A7367G", + "G9080A", + "T9341C", + "C10967T", + "A11991G" + ], + "F": [ + "P520S" ], "G": [ - "S181N" + "K75R" ], "L": [ - "S534N" + "I1609V" ] }, "labels": { - "aa": "G: S181N; L: S534N" + "aa": "F: P520S; G: K75R; L: I1609V" } } }, { - "name": "NODE_0000497", + "name": "OP904095", "node_attrs": { - "div": 0.152, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -57666,142 +58278,37 @@ "branch_attrs": { "mutations": { "nuc": [ - "G5072A", - "A7086G", - "T8570A", - "C11730T" + "A4239G", + "A5906G", + "G6715A", + "G7214A", + "T8606C", + "A9460G", + "A9860T", + "A10233G", + "T12626C" + ], + "G": [ + "V157I" + ], + "L": [ + "K765R", + "R898S", + "I1023V" + ], + "SH": [ + "N138S" ] - } - }, - "children": [ - { - "name": "OP345082", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G270A", - "C657T", - "A1307G", - "T1395C", - "T1406C", - "G1496A", - "T1709A", - "T1725C", - "A2976G", - "A3729G", - "G3894A", - "T4158C", - "G4549A", - "T5802C", - "T5903C", - "C6016T", - "T6441C", - "T6495C", - "C6564T", - "A6574G", - "G6578A", - "T6864C", - "C8304T", - "A8321T", - "G8393A", - "C8564T", - "A8615G", - "T8681C", - "G9722A", - "T10094C", - "A10367T", - "C10772T", - "G11669A", - "G12128A" - ], - "F": [ - "V500I" - ], - "G": [ - "M110V", - "S111N" - ], - "P": [ - "D154E" - ], - "SH": [ - "I137T", - "H175Y" - ] - }, - "labels": { - "aa": "F: V500I; G: M110V, S111N; P: D154E; SH: I137T, H175Y" - } - } }, - { - "name": "MZ851796", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1131T", - "T1555C", - "G2018A", - "A2698G", - "T2965C", - "A3330G", - "C4335T", - "G4377A", - "T4468C", - "C4811T", - "T5786C", - "G5926A", - "A6466T", - "T6633C", - "T6711C", - "G7137A", - "A7164G", - "C7775T", - "G8011A", - "A9484G", - "T11179C", - "G13199A", - "T13240C" - ], - "G": [ - "N74Y" - ], - "L": [ - "R282K", - "K773R", - "I1338T" - ], - "P": [ - "L103P" - ], - "SH": [ - "I98T", - "D145N" - ] - }, - "labels": { - "aa": "G: N74Y; L: R282K, K773R, I1338T; P: L103P; SH: I98T, D145N" - } - } + "labels": { + "aa": "G: V157I; L: K765R, R898S, I1023V; SH: N138S" } - ] + } } ] }, { - "name": "NODE_0000498", + "name": "NODE_0000504", "node_attrs": { "div": 0.152, "clade_membership": { @@ -57811,32 +58318,29 @@ "branch_attrs": { "mutations": { "nuc": [ - "T336A", - "C942A", - "A1850G", - "T2896C", - "C2930T", - "C2942T", - "G3513A", - "C4925T", - "A5352G", - "G7370A", - "G8903A", - "C12962T" + "G2015A", + "G5922A", + "G6033A", + "T6300C", + "C6782T", + "T6823C", + "T6852C", + "T12527C", + "T12578C" ], - "L": [ - "M68I" + "G": [ + "S193P" ] }, "labels": { - "aa": "L: M68I" + "aa": "G: S193P" } }, "children": [ { - "name": "PP947676", + "name": "PP947696", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -57844,80 +58348,81 @@ "branch_attrs": { "mutations": { "nuc": [ - "C209T", - "G264A", - "C675A", - "G816A", - "A861T", - "G1339A", - "G2180A", - "C2258T", - "G2614A", - "C2936A", - "C3006A", - "A3357G", - "T3453C", - "T3624C", - "T3705C", - "T4563C", - "T4587C", - "C4919T", - "G4970A", - "C5696T", - "G5793A", - "C5820T", - "G5837T", - "C5951T", - "T6131A", - "C6402T", - "T6864C", - "A7081T", - "A7184G", - "G7488A", - "G8118T", - "T8210C", - "G8692A", - "A8778G", - "T9176C", - "C9629T", - "T10490A", - "G11192A", - "T11204C", - "C12755T", - "C12965T" - ], - "L": [ - "G108S", - "G318C", - "S509N", - "R538G" + "T456C", + "T513C", + "A858G", + "C1203T", + "G1253T", + "C1335T", + "T1593C", + "T1613C", + "G1667A", + "A2260C", + "G2440A", + "A2602G", + "T2752C", + "C2953T", + "C4570T", + "G5072A", + "G5299A", + "G5598A", + "T5787C", + "T5802C", + "G6044A", + "G6048A", + "A6157T", + "T6159A", + "T6163-", + "A6164-", + "A6165-", + "T6342A", + "C6378T", + "G6446A", + "C6656T", + "C6761T", + "G6862A", + "G6880A", + "C6958T", + "A6981T", + "G6991A", + "A7083G", + "C7097T", + "T9071C", + "T9527C", + "A9539G", + "A9941G", + "A10151G", + "C10337T", + "T11750C", + "C12119T", + "T12191C", + "A12749G", + "T12758C", + "T13217C" ], - "M": [ - "V6I", - "M150I" + "G": [ + "S67N", + "P137L", + "P172L", + "G206S", + "A212T" ], - "N": [ - "T57I", - "D212E" + "M2-2": [ + "E18K" ], "P": [ - "S31N" - ], - "SH": [ - "P68L", - "S115I", - "P153L" + "P30S" ] }, "labels": { - "aa": "L: G108S, G318C, S509N, R538G; M: V6I, M150I; N: T57I, D212E; P: S31N; SH: P68L, S115I, P153L" + "aa": "G: S67N, P137L, P172L, G206S, A212T; M2-2: E18K; P: P30S" } } }, { - "name": "NODE_0000499", + "name": "NODE_0000505", "node_attrs": { - "div": 0.153, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -57925,23 +58430,50 @@ "branch_attrs": { "mutations": { "nuc": [ - "A6674G", - "G13082A" + "A2359G", + "T3303C", + "C5537T", + "G5583A", + "T5600C", + "T5615C", + "T5649C", + "T6019C", + "C6454T", + "T6491C", + "C6551T", + "A6616G", + "A6943G", + "A7020G", + "T7292C", + "C8342T", + "T9353A", + "A10485G" ], "G": [ - "I153T", - "F162L" + "P70S", + "I82T", + "P102L", + "T124A" + ], + "L": [ + "I1107V" + ], + "SH": [ + "T15I", + "L36S", + "L41P", + "Y176H" ] }, "labels": { - "aa": "G: I153T, F162L" + "aa": "G: P70S, I82T, P102L, T124A; L: I1107V; SH: T15I, L36S, L41P, Y176H" } }, "children": [ { - "name": "PP947607", + "name": "OP358285", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -57949,61 +58481,65 @@ "branch_attrs": { "mutations": { "nuc": [ - "T91C", - "C1017A", - "C1134T", - "G1664A", - "T1994C", - "T2086G", - "C2318T", - "C2563T", - "G3150A", - "G3278A", - "T3405A", - "C3747T", - "T4742A", - "C6552T", - "C6850T", - "C7217T", - "T7517G", - "T7527C", - "C7982T", - "T8519A", - "A9186G", - "T9863C", - "A10016T", - "A10046G", - "G10091A", - "T11084A", - "G11285A", - "T11307C", - "C12473T", - "G12686A", - "A13203G", - "A13251G" - ], - "F": [ - "S76N" + "T5485C", + "T5514C", + "T5585C", + "T5622C", + "T5623C", + "T5630C", + "T5651C", + "T5730C", + "T5750C", + "T5770C", + "T5794C", + "T5807C", + "T5834C", + "T5883C", + "A6033G", + "T6328C", + "T6329C", + "T6359C", + "T6384C", + "T6388C", + "T6392C", + "T6398C", + "T6410C", + "T6441C", + "T6524C", + "T6887C", + "T6999C", + "T7028C" ], "G": [ - "H202Y" - ], - "L": [ - "D117E", - "M674V", - "L950F" + "F28P", + "I38T", + "Y48H", + "L49P", + "I51T", + "I55T", + "L93P", + "F162L", + "V214A" ], - "P": [ - "L280R" + "SH": [ + "L31P", + "F44L", + "V46A", + "I53T", + "L86P", + "Y93H", + "Y101H", + "V105A", + "I114T" ] }, "labels": { - "aa": "F: S76N; G: H202Y; L: D117E, M674V, L950F; P: L280R" + "aa": "G: F28P, I38T, Y48H, L49P, I51T, I55T, L93P, F162L, V214A; SH: L31P, F44L, V46A, I53T, L86P, Y93H, Y101H, V105A, I114T" } } }, { - "name": "NODE_0000500", + "name": "OP358284", "node_attrs": { "div": 0.154, "clade_membership": { @@ -58011,78 +58547,8 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C996T", - "G1476A", - "T1883C", - "G3936A", - "C3958T", - "G5918A", - "T6711C", - "C6802T", - "G6897A", - "A7226T", - "C8726T", - "A8780G", - "C8990T", - "T9671C", - "A10044G", - "G10454A", - "G10488A", - "A11990T", - "C12924A" - ], - "G": [ - "P186S", - "M217I" - ], - "L": [ - "T960A", - "V1108I", - "L1920I" - ], - "P": [ - "A77T" - ], - "SH": [ - "R142K" - ] - }, - "labels": { - "aa": "G: P186S, M217I; L: T960A, V1108I, L1920I; P: A77T; SH: R142K" - } - }, - "children": [ - { - "name": "PP947698", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G2984A" - ] - } - } - }, - { - "name": "PP947669", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + "mutations": {} + } } ] } @@ -58091,9 +58557,9 @@ ] }, { - "name": "NODE_0000501", + "name": "NODE_0000506", "node_attrs": { - "div": 0.151, + "div": 0.152, "clade_membership": { "value": "A2b2" } @@ -58101,21 +58567,33 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6887T" + "T1511G", + "A5619G", + "G6296A", + "T6372C", + "C6405T", + "G8156A", + "C10530T", + "C12278T", + "C12611T" ], "G": [ - "A214V" + "R17K", + "F162L" + ], + "P": [ + "I88M" ] }, "labels": { - "aa": "G: A214V" + "aa": "G: R17K, F162L; P: I88M" } }, "children": [ { - "name": "NODE_0000502", + "name": "NODE_0000507", "node_attrs": { - "div": 0.151, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -58123,15 +58601,18 @@ "branch_attrs": { "mutations": { "nuc": [ - "T3627C" + "T6730C", + "C7448T", + "A11879G", + "G13239A" ] } }, "children": [ { - "name": "NODE_0000503", + "name": "MZ851992", "node_attrs": { - "div": 0.153, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -58139,123 +58620,40 @@ "branch_attrs": { "mutations": { "nuc": [ - "G346A", - "T1725C", - "A2027G", - "C2148-", - "C3846T", - "T6042C", - "T6153C", - "T6160C", - "T6167C", - "T6168C", - "T6190C", - "T6206C", - "T6213C", - "T6607C", - "C7556T", - "C8240T", - "A8303G", - "G9476A", - "T10051A", - "A10073G" + "C1554T", + "C2045T", + "T5928C", + "T6030C", + "A6150G", + "A6305G", + "A6417G", + "G6610A", + "T6807C", + "A6848G", + "T6864C", + "T6887C", + "A9260C", + "G11072A" ], "G": [ - "S121P" + "N20S", + "D122N", + "N201S", + "V214A" ], "L": [ - "I962K" - ], - "N": [ - "V103I" + "E698D" ] }, "labels": { - "aa": "G: S121P; L: I962K; N: V103I" - } - }, - "children": [ - { - "name": "OP904095", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A4239G", - "A5906G", - "G6715A", - "G7214A", - "T8606C", - "A9460G", - "A9860T", - "A10233G", - "T12626C" - ], - "G": [ - "V157I" - ], - "L": [ - "K765R", - "R898S", - "I1023V" - ], - "SH": [ - "N138S" - ] - }, - "labels": { - "aa": "G: V157I; L: K765R, R898S, I1023V; SH: N138S" - } - } - }, - { - "name": "OP904096", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C4233T", - "C4609T", - "G6145A", - "A6470G", - "T6965C", - "A7367G", - "G9080A", - "T9341C", - "C10967T", - "A11991G" - ], - "F": [ - "P520S" - ], - "G": [ - "K75R" - ], - "L": [ - "I1609V" - ] - }, - "labels": { - "aa": "F: P520S; G: K75R; L: I1609V" - } - } + "aa": "G: N20S, D122N, N201S, V214A; L: E698D" } - ] + } }, { - "name": "NODE_0000504", + "name": "MN745086", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -58263,246 +58661,33 @@ "branch_attrs": { "mutations": { "nuc": [ - "G2015A", - "G5922A", - "G6033A", - "T6300C", - "C6782T", - "T6823C", - "T6852C", - "T12527C", - "T12578C" + "G1928A", + "C2563T", + "G4254A", + "C5593T", + "C6898T", + "A10283G", + "T12674C" ], "G": [ - "S193P" + "Q218*" + ], + "L": [ + "I1039M" + ], + "SH": [ + "L34F" ] }, "labels": { - "aa": "G: S193P" - } - }, - "children": [ - { - "name": "PP947696", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T456C", - "T513C", - "A858G", - "C1203T", - "G1253T", - "C1335T", - "T1593C", - "T1613C", - "G1667A", - "A2260C", - "G2440A", - "A2602G", - "T2752C", - "C2953T", - "C4570T", - "G5072A", - "G5299A", - "G5598A", - "T5787C", - "T5802C", - "G6044A", - "G6048A", - "A6157T", - "T6159A", - "T6163-", - "A6164-", - "A6165-", - "T6342A", - "C6378T", - "G6446A", - "C6656T", - "C6761T", - "G6862A", - "G6880A", - "C6958T", - "A6981T", - "G6991A", - "A7083G", - "C7097T", - "T9071C", - "T9527C", - "A9539G", - "A9941G", - "A10151G", - "C10337T", - "T11750C", - "C12119T", - "T12191C", - "A12749G", - "T12758C", - "T13217C" - ], - "G": [ - "S67N", - "P137L", - "P172L", - "G206S", - "A212T" - ], - "M2-2": [ - "E18K" - ], - "P": [ - "P30S" - ] - }, - "labels": { - "aa": "G: S67N, P137L, P172L, G206S, A212T; M2-2: E18K; P: P30S" - } - } - }, - { - "name": "NODE_0000505", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A2359G", - "T3303C", - "C5537T", - "G5583A", - "T5600C", - "T5615C", - "T5649C", - "T6019C", - "C6454T", - "T6491C", - "C6551T", - "A6616G", - "A6943G", - "A7020G", - "T7292C", - "C8342T", - "T9353A", - "A10485G" - ], - "G": [ - "P70S", - "I82T", - "P102L", - "T124A" - ], - "L": [ - "I1107V" - ], - "SH": [ - "T15I", - "L36S", - "L41P", - "Y176H" - ] - }, - "labels": { - "aa": "G: P70S, I82T, P102L, T124A; L: I1107V; SH: T15I, L36S, L41P, Y176H" - } - }, - "children": [ - { - "name": "OP358285", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T5485C", - "T5514C", - "T5585C", - "T5622C", - "T5623C", - "T5630C", - "T5651C", - "T5730C", - "T5750C", - "T5770C", - 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"T1511G", - "A5619G", - "G6296A", - "T6372C", - "C6405T", - "G8156A", - "C10530T", - "C12278T", - "C12611T" - ], - "G": [ - "R17K", - "F162L" - ], - "P": [ - "I88M" - ] - }, - "labels": { - "aa": "G: R17K, F162L; P: I88M" - } + "mutations": {} }, "children": [ { - "name": "NODE_0000507", + "name": "OP345077", "node_attrs": { - "div": 0.152, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -58546,93 +58709,51 @@ "branch_attrs": { "mutations": { "nuc": [ - "T6730C", - "C7448T", - "A11879G", - "G13239A" + "G825A", + "C1505T", + "T2003C", + "T2728C", + "C3166T", + "C3222T", + "A3559G", + "C3597T", + "A3852G", + "C4107T", + "T4530C", + "G5072A", + "G5380A", + "G5694A", + "C5864T", + "A7502G", + "G7802A", + "C7982T", + "G8755A", + "C10289T", + "C11576T", + "T11981C", + "T12206C", + "C12897T" + ], + "F": [ + "S170G" + ], + "L": [ + "R530K" + ], + "M2-2": [ + "G45R" + ], + "SH": [ + "T124I" ] - } - }, - "children": [ - { - "name": "MZ851992", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C1554T", - "C2045T", - "T5928C", - "T6030C", - "A6150G", - "A6305G", - "A6417G", - "G6610A", - "T6807C", - "A6848G", - "T6864C", - "T6887C", - "A9260C", - "G11072A" - ], - "G": [ - "N20S", - "D122N", - "N201S", - "V214A" - ], - "L": [ - "E698D" - ] - }, - "labels": { - "aa": "G: N20S, D122N, N201S, V214A; L: E698D" - } - } }, - { - "name": "MN745086", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G1928A", - "C2563T", - "G4254A", - "C5593T", - "C6898T", - "A10283G", - "T12674C" - ], - "G": [ - "Q218*" - ], - "L": [ - "I1039M" - ], - "SH": [ - "L34F" - ] - }, - "labels": { - "aa": "G: Q218*; L: I1039M; SH: L34F" - } - } + "labels": { + "aa": "F: S170G; L: R530K; M2-2: G45R; SH: T124I" } - ] + } }, { - "name": "NODE_0000508", + "name": "NODE_0000509", "node_attrs": { "div": 0.152, "clade_membership": { @@ -58644,7 +58765,7 @@ }, "children": [ { - "name": "OP345077", + "name": "OP904008", "node_attrs": { "div": 0.154, "clade_membership": { @@ -58654,51 +58775,51 @@ "branch_attrs": { "mutations": { "nuc": [ - "G825A", - "C1505T", - "T2003C", - "T2728C", - "C3166T", - "C3222T", - "A3559G", - "C3597T", - "A3852G", - "C4107T", - "T4530C", - "G5072A", - "G5380A", - "G5694A", - "C5864T", - "A7502G", - "G7802A", - "C7982T", - "G8755A", - "C10289T", - "C11576T", - "T11981C", - "T12206C", - "C12897T" + "G279A", + "G1448A", + "C2148-", + "T4074C", + "G4188A", + "C4368T", + "A4488G", + "A4649G", + "G5328A", + "T5957C", + "A6161G", + "T6189C", + "C6286T", + "T6441C", + "T6489C", + "T6626C", + "T6633C", + "T6978C", + "A7008G", + "C8102T", + "C8123T", + "C8184T", + "C10610T", + "A11453G", + "C11876T", + "G12131A" ], "F": [ - "S170G" + "N533S" ], - "L": [ - "R530K" - ], - "M2-2": [ - "G45R" + "G": [ + "L14F", + "L127P" ], "SH": [ - "T124I" + "V155A" ] }, "labels": { - "aa": "F: S170G; L: R530K; M2-2: G45R; SH: T124I" + "aa": "F: N533S; G: L14F, L127P; SH: V155A" } } }, { - "name": "NODE_0000509", + "name": "NODE_0000510", "node_attrs": { "div": 0.152, "clade_membership": { @@ -58708,14 +58829,13 @@ "branch_attrs": { "mutations": { "nuc": [ - "C2148-", "A13308G" ] } }, "children": [ { - "name": "OP904008", + "name": "NODE_0000511", "node_attrs": { "div": 0.154, "clade_membership": { @@ -58725,62 +58845,45 @@ "branch_attrs": { "mutations": { "nuc": [ - "G279A", - "G1448A", - "T4074C", - "G4188A", - "C4368T", - "A4488G", - "A4649G", - "G5328A", - "T5957C", - "A6161G", - "T6189C", - "C6286T", - "T6441C", - "T6489C", - "T6626C", - "T6633C", - "T6978C", - "A7008G", - "C8102T", - "C8123T", - "C8184T", - "C10610T", - "A11453G", - "C11876T", - "G12131A" - ], - "F": [ - "N533S" + "G117A", + "A632T", + "T1140A", + "C1910T", + "G2937A", + "C3597T", + "T4227C", + "G4470A", + "A4473T", + "C5679T", + "C5916T", + "T6300C", + "A6432G", + "G6637A", + "G6798A", + "A6888G", + "T6992C", + "T6999C", + "A7127G", + "C7199T", + "C8414A", + "A8579G", + "C10806T", + "A13151G" ], "G": [ - "L14F", - "L127P" + "D131N" ], - "SH": [ - "V155A" + "N": [ + "Y198F" ] }, "labels": { - "aa": "F: N533S; G: L14F, L127P; SH: V155A" + "aa": "G: D131N; N: Y198F" } - } - }, - { - "name": "NODE_0000510", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} }, "children": [ { - "name": "NODE_0000511", + "name": "OP345080", "node_attrs": { "div": 0.154, "clade_membership": { @@ -58790,46 +58893,41 @@ "branch_attrs": { "mutations": { "nuc": [ - "G117A", - "A632T", - "T1140A", - "C1910T", - "-2148C", - "G2937A", - "C3597T", - "T4227C", - "G4470A", - "A4473T", - "C5679T", - "C5916T", - "T6300C", - "A6432G", - "G6637A", - "G6798A", - "A6888G", - "T6992C", - "T6999C", - "A7127G", - "C7199T", - "C8414A", - "A8579G", - "C10806T", - "A13151G" + "C481A", + "G7019A", + "A11835G" ], - "G": [ - "D131N" + "L": [ + "I1557V" ], "N": [ - "Y198F" + "Q148K" ] }, "labels": { - "aa": "G: D131N; N: Y198F" + "aa": "L: I1557V; N: Q148K" + } + } + }, + { + "name": "NODE_0000512", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A687G", + "A2569G" + ] } }, "children": [ { - "name": "OP345080", + "name": "OP345079", "node_attrs": { "div": 0.154, "clade_membership": { @@ -58837,26 +58935,11 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C481A", - "G7019A", - "A11835G" - ], - "L": [ - "I1557V" - ], - "N": [ - "Q148K" - ] - }, - "labels": { - "aa": "L: I1557V; N: Q148K" - } + "mutations": {} } }, { - "name": "NODE_0000512", + "name": "NODE_0000513", "node_attrs": { "div": 0.154, "clade_membership": { @@ -58864,100 +58947,99 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A687G", - "A2569G" - ] - } + "mutations": {} }, "children": [ { - "name": "OP345079", + "name": "OP345078", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } - }, - "branch_attrs": { - "mutations": {} + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T2060C", + "T2086C", + "T2203C", + "C12438A", + "T13218G" + ], + "L": [ + "Q1758K" + ], + "P": [ + "L280P" + ] + }, + "labels": { + "aa": "L: Q1758K; P: L280P" + } } }, { - "name": "NODE_0000513", + "name": "MN745087", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "OP345078", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T2060C", - "T2086C", - "T2203C", - "C12438A", - "T13218G" - ], - "L": [ - "Q1758K" - ], - "P": [ - "L280P" - ] - }, - "labels": { - "aa": "L: Q1758K; P: L280P" - } - } + "mutations": { + "nuc": [ + "C6898T", + "A10139G" + ], + "G": [ + "Q218*" + ] }, - { - "name": "MN745087", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C6898T", - "A10139G" - ], - "G": [ - "Q218*" - ] - }, - "labels": { - "aa": "G: Q218*" - } - } + "labels": { + "aa": "G: Q218*" } - ] + } } ] } ] + } + ] + }, + { + "name": "NODE_0000514", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C2946T", + "C3381T", + "T6575C", + "A6903T", + "T8762C", + "A11246T" + ], + "G": [ + "M110T", + "K219N" + ] }, + "labels": { + "aa": "G: M110T, K219N" + } + }, + "children": [ { - "name": "NODE_0000514", + "name": "OP904029", "node_attrs": { - "div": 0.152, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -58965,27 +59047,70 @@ "branch_attrs": { "mutations": { "nuc": [ - "C2946T", - "C3381T", - "T6575C", - "A6903T", - "T8762C", - "A11246T" + "G204A", + "A807G", + "C1730T", + "C2148-", + "G2308A", + "C2485T", + "C2729T", + "G2917T", + "G3528A", + "G3810A", + "C3882T", + "G6075A", 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+ "name": "OP904176", "node_attrs": { - "div": 0.153, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -59063,27 +59188,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "-2148C", - "G3666A", - "A4384G", - "G4546A", - "C6456A", - "C8240T" - ], - "F": [ - "S445G", - "A499T" + "T5649C" ] - }, - "labels": { - "aa": "F: S445G, A499T" } } }, { - "name": "NODE_0000516", + "name": "NODE_0000517", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -59091,41 +59204,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C558T", - "T1313C", - "T1337C", - "T1395C", - "T1401C", - "T1520C", - "T1555C", - "T1562C", - "T1626A", - "C2287T", - "C3531T", - "C4299T", - "C5036T", - "G5477A", - "C5724T", - "T6070C", - "C6761T", - "C6789T", - "G7463A", - "G13121A" - ], - "P": [ - "L103P", - "S127T" + "C7014A" ] - }, - "labels": { - "aa": "P: L103P, S127T" } }, "children": [ { - "name": "OP904176", + "name": "OP904031", "node_attrs": { - "div": 0.154, + "div": 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"node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "G5752A", + "A6261G", + "A7014G", + "A7072G" + ], + "SH": [ + "D87N" + ] + }, + "labels": { + "aa": "SH: D87N" + } + } + }, + { + "name": "NODE_0000520", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A1649G", + "A5781T", + "C6572T" + ], + "G": [ + "S109L" + ], + "SH": [ + "R96S" + ] + }, + "labels": { + "aa": "G: S109L; SH: R96S" + } }, "children": [ { - "name": "OP904031", + "name": "OP904010", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C4609T", - "G7066A", - "G7892A" - ], - "F": [ - "P520S" - ] - }, - "labels": { - "aa": "F: P520S" - } + "mutations": {} } }, { - "name": "NODE_0000520", + "name": "OP904007", "node_attrs": { - "div": 0.154, + 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"NODE_0000522", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -59295,9 +59374,9 @@ }, "children": [ { - "name": "OP904175", + "name": "OP904181", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -59307,9 +59386,9 @@ } }, { - "name": "NODE_0000522", + "name": "NODE_0000523", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -59321,7 +59400,7 @@ { "name": "OP904180", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -59331,42 +59410,16 @@ } }, { - "name": "NODE_0000523", + "name": "OP904030", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { "mutations": {} - }, - "children": [ - { - "name": "OP904181", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "OP904030", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + } } ] } @@ -59397,11 +59450,104 @@ ] } ] + } + ] + }, + { + "name": "NODE_0000524", + "node_attrs": { + "div": 0.151, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G3315A", + "T5595C", + "C9614T", + "T9843C" + ] + } + }, + "children": [ + { + "name": "LC671556", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T1406C", + "C1925T", + "C2242T", + "C3102T", + "C3225T", + "T3930A", + "C4557T", + "C5749T", + "G5926A", + "G5953A", + "A6324G", + "T6711C", + "G6779A", + "C6887T", + "G6897A", + "A6901G", + "C6998A", + "T6999C", + "C7074A", + "T7135C", + "G7353A", + "T8555A", + "G8651A", + "C8699T", + "G8975A", + "T9533C", + "G9644A", + "T10055C", + "C10205T", + "T10667C", + "G11168A", + "G11372A", + "A11417G", + 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"NODE_0000531", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -59528,35 +60031,37 @@ "branch_attrs": { "mutations": { "nuc": [ - "T348C", - "T1158A", - "T1406C", - "G2018A", - "T2033G", - "T2341C", - "A5885C", - "T6343C", - "T6477C", - "C7088T", - "T7089C", - "G11354A", - "C12164T", - "T12881C" - ], - "N": [ - "D373E" + "T1033C", + "C2866T", + "C3102T", + "A3543G", + "T5574C", + "C5696A", + "C6720T", + "G7082A", + "G7085T", + "A7086T", + "A7087C", + "T7090C", + "T7487C", + "C7557T", + "A8030G", + "G9581A", + "G9695A", + "C10988T", + "C11426T" ], "SH": [ - "K131T" + "P68Q" ] }, "labels": { - "aa": "N: D373E; SH: K131T" + "aa": "SH: P68Q" } }, "children": [ { - "name": "NODE_0000527", + "name": "PP947700", "node_attrs": { "div": 0.154, "clade_membership": { @@ -59566,100 +60071,34 @@ "branch_attrs": { "mutations": { "nuc": [ - "C252T", - "G582A", - "C1568T", - "C1606T", - "T2060C", - "C2148-", - "A2236G", - "C2342T", - "C2656T", - "C2740T", - 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"branch_attrs": { - "mutations": { - "nuc": [ - "C657T" - ] - } - } + "aa": "G: S101N, P186S; P: S31N" } - ] + } }, { - "name": "NODE_0000528", + "name": "PP947685", "node_attrs": { "div": 0.155, "clade_membership": { @@ -59669,138 +60108,117 @@ "branch_attrs": { "mutations": { "nuc": [ - "A23C", - "T774C", - "A861G", - "T969C", - "C1032T", - "A1500G", - "G1589A", - "C2942T", - "G3813A", - "A5210G", - "A5555G", - "G5682A", - "T5913C", - "G6121A", - "C6143T", - "T6213C", - "A6681T", - "C6760T", - "C6777A", - "C6791T", - "G6817A", - "G6853A", - "C6927T", - "C7054T", - "C8106A", - "A8384G", - "C8426T", - "C8462T", - "C8480T", - "A10439G", - "T10854C", - "A10961G", - "A11527G", - "A11744C", - "G11786A", - "A12947G", - "G13260A" + "G204A", + "A570G", + "T1395C", + "T1406C", + "G1685A", + "G1790A", + "T1862C", + "C2084T", + "G2914A", + "C3381T", + "T6430C", + "C6579T", + "T6621C", + "C6655T", + "C6690T", + "A7581G", + "T7586C", + "A8066G", + "T10124C", + "A10154G", + "A10718G", + "A12076G" ], "G": [ - "A182V", - "V191I", - "E203K" + "S62P", + "P137S" ], "L": [ - "L314I", - "K1454R" + "I139V", + "D1637G" + ] + }, + "labels": { + "aa": "G: S62P, P137S; L: I139V, D1637G" + } + } + } + ] + }, + { + "name": "NODE_0000532", + "node_attrs": { + "div": 0.152, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ + { + "name": "NODE_0000533", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C294T", + "G315A", + "T1053C", + "G1233A", + "T1492C", + "T1538C", + "T1631C", + "T3405C", + "G3408A", + "T3453C", + "T3462C", + "T3627C", + "G4796A", + "C4901T", + "C4961T", + "C5904T", + "C6655T", + "C6789T", + "G7104T", + "T7178C", + "C7556T", + "T8210C", + "G8360A", + "G8879A", + "T8945C", + "T9176C", + "G9686A", + "C11159T", + "C11357T", + "C12362T", + "T12812C", + "C13213T", + "T13306C", + "A13321G" ], - "P": [ - "T85A" + "G": [ + "P137S" ], - 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D145N" - } - } - }, - { - "name": "NODE_0000529", + "name": "NODE_0000534", "node_attrs": { "div": 0.156, "clade_membership": { @@ -59810,32 +60228,41 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1047C", - "G2836A", - "C2957T", - "C4056T", - "A7071G", - "C7625T", - "C7769T", - "G9867A", - "T9962C", - "A10664T", - "C10967T", - "A11291G", - "G11753A", - "C12105T" + "C324T", + "T2033C", + "C2455T", + "C2942T", + "T3141C", + "C3166T", + "T4518A", + "A5180G", + "C5934T", + "A6685T", + "C6887A", + "A6895G", + "T7832C", + "C8304T", + "T9095C", + "G11777A", + "A12059G", + "G12863A" ], - "L": [ - "E901K" + "G": [ + "T147S", + "A214E", + "M217-", + "Q218-", + "K219-", + "*220-" ] }, "labels": { - "aa": "L: E901K" + "aa": "G: T147S, A214E, M217-, Q218-, K219-, *220-" } }, "children": [ { - "name": "OR883672", + "name": "PP947618", "node_attrs": { "div": 0.156, "clade_membership": { @@ -59845,27 +60272,23 @@ "branch_attrs": { "mutations": { "nuc": [ - "G939A", - "C7207T", - "A11210T", - "G11366A" - ], - "G": [ - "P172S" + "A1881G", + "G3035A", + "A3963G" ], - "L": [ - "P14L" + "P": [ + "I212V" ] }, "labels": { - "aa": "G: P172S; L: P14L" + "aa": "P: I212V" } } }, { - "name": "OR671979", + "name": "PP947599", "node_attrs": { - "div": 0.158, + "div": 0.157, "clade_membership": { "value": "A2b2" } @@ -59873,241 +60296,30 @@ "branch_attrs": { "mutations": { "nuc": [ - "C24-", - "G51A", - "G54A", - "A345G", - "T370C", - "C3639T", - "T4359A", - "A4600G", - "G5241A", - "C5265T", - "C5562A", - "T5910C", - "C6381T", - "T6489C", - "T6491C", - "T6524C", - "T6575C", - "T6583C", - "C6630T", - "T6635C", - "A7343G", - "C8327T", - "G9480A", - "T9611C", - "T9774C", - "A9874G", - "C10384T", - "G11747A", - "C12713T" - ], - "F": [ - "T517A" - ], - "G": [ - "I82T", - "L93P", - "V110A", - "S113P", - "V130A" + "A885G", + "C6516T", + "A7887G", + "T9398C", + "A10026G", + "C12278T", + "C12971T" ], "L": [ - "V772I", - "K903R", - "T1073I" - ], - "M2-1": [ - "A169T" + "N241D", + "T954A" ] }, "labels": { - "aa": "F: T517A; G: I82T, L93P, V110A, S113P, V130A; L: V772I, K903R, T1073I; M2-1: A169T" + "aa": "L: N241D, T954A" } } } ] - } - ] - } - ] - }, - { - "name": "NODE_0000530", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A690G", - "C1806T", - "G3495A", - "A6333G", - "T6628C", - "T7829C", - "C8192T", - "G10553A", - "C10853A", - "C12962T", - "G13211A" - ], - "G": [ - "S128P" - ] - }, - "labels": { - "aa": "G: S128P" - } - }, - "children": [ - { - "name": "NODE_0000531", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1033C", - "C2866T", - "C3102T", - "A3543G", - "T5574C", - "C5696A", - "C6720T", - "G7082A", - "G7085T", - "A7086T", - "A7087C", - "T7090C", - "T7487C", - "C7557T", - "A8030G", - "G9581A", - "G9695A", - "C10988T", - "C11426T" - ], - "SH": [ - "P68Q" - ] - }, - "labels": { - "aa": "SH: 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"A13232G" ], - "P": [ - "V82A" + "F": [ + "V500I" ] }, "labels": { - "aa": "G: P137S; P: V82A" + "aa": "F: V500I" } }, "children": [ { - "name": "NODE_0000534", + "name": "PP947641", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -60173,41 +60360,42 @@ "branch_attrs": { "mutations": { "nuc": [ - "C324T", - "T2033C", - "C2455T", - "C2942T", - "T3141C", + "A2097G", "C3166T", - "T4518A", - "A5180G", - "C5934T", - "A6685T", - "C6887A", - "A6895G", - "T7832C", - "C8304T", - "T9095C", - "G11777A", - "A12059G", - "G12863A" + "A6404C", + "T6904C" ], "G": [ - "T147S", - "A214E", - "M217-", - "Q218-", - "K219-", - "*220-" + "Y53S", + "*220Q" + ], + "P": [ + "N284D" ] }, "labels": { - "aa": "G: T147S, A214E, M217-, Q218-, K219-, *220-" + "aa": "G: Y53S, *220Q; P: N284D" + } + } + }, + { + "name": "NODE_0000536", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A4862G" + ] } }, "children": [ { - "name": "PP947618", + "name": "PP947699", "node_attrs": { "div": 0.156, "clade_membership": { @@ -60217,21 +60405,26 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1881G", - "G3035A", - "A3963G" + "C741T", + "T4526C", + "C4934T", + "A5424C", + "C11201T" ], - "P": [ - "I212V" + "F": [ + "I492T" + ], + "M2-2": [ + "E59D" ] }, "labels": { - "aa": "P: I212V" + "aa": "F: I492T; M2-2: E59D" } } }, { - "name": "PP947599", + "name": "PP947661", "node_attrs": { "div": 0.156, "clade_membership": { @@ -60241,30 +60434,119 @@ "branch_attrs": { "mutations": { "nuc": [ - "A885G", - "C6516T", - "A7887G", - "T9398C", - "A10026G", - "C12278T", - "C12971T" + "G1892A", + "G3813A", + "A5518C", + "G6835A", + "C6836T", + "G7694A", + "A8468G" ], - "L": [ - "N241D", - "T954A" + "G": [ + "A197I" + ], + "SH": [ + "N9H" ] }, "labels": { - "aa": "L: N241D, T954A" + "aa": "G: A197I; SH: N9H" } } } ] + } + ] + } + ] + }, + { + "name": "NODE_0000537", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T285C", + "G1451A", + "G3009A", + "A3636G", + "A4290G", + "A6148G", + "G11336A", + "C11492T", + "G11495A", + "C12704T" + ] + } + }, + "children": [ + { + "name": "NODE_0000538", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ + { + "name": "MZ851993", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A171T", + "C563T", + "G2556T", + "G2981A", + "G3564A", + "C3609T", + "-4692G", + "-4693T", + "A4720-", + "T4721-", + "C4745T", + "A5631G", + "C6000T", + "C7144T", + "A9122G", + "G10498A", + "G11900A", + "G12779A", + "C13332T" + ], + "L": [ + "S1111N" + ], + "M": [ + "S131I" + ], + "N": [ + "T175I" + ] + }, + "labels": { + "aa": "L: S1111N; M: S131I; N: T175I" + } + } }, { - "name": "NODE_0000535", + "name": "NODE_0000539", "node_attrs": { - "div": 0.155, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -60272,32 +60554,23 @@ "branch_attrs": { "mutations": { "nuc": [ - "T804C", - "C4299T", - "G4344A", - "G4512A", - "G4549A", - "T5075C", - "T5081C", - "A8171G", - "T8202C", - "C8399T", - "A9515G", - "A13232G" + "G5793A", + "C5972T", + "C7096T" ], - "F": [ - "V500I" + "SH": [ + "T160I" ] }, "labels": { - "aa": "F: V500I" + "aa": "SH: T160I" } }, "children": [ { - "name": "PP947641", + "name": "NODE_0000540", "node_attrs": { - "div": 0.155, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -60305,42 +60578,40 @@ "branch_attrs": { "mutations": { "nuc": [ - "A2097G", - "C3166T", - "A6404C", - "T6904C" + "T2428C", + "A4380G", + "G4496A", + "T5075C", + "C6068T", + "C6767T", + "G6994A", + "T7103C", + "T7109C", + "T7131C", + "T7135C", + "G7136A", + "A7262G", + "C7490T", + "T10217C", + "A10322G", + "G11840A", + "G12863A", + "C12987T" ], - "G": [ - "Y53S", - "*220Q" + "F": [ + "S482N" ], - "P": [ - "N284D" + "G": [ + "P172S" ] }, "labels": { - "aa": "G: Y53S, *220Q; P: N284D" - } - } - }, - { - "name": "NODE_0000536", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A4862G" - ] + "aa": "F: S482N; G: P172S" } }, "children": [ { - "name": "PP947699", + "name": "PP947651", "node_attrs": { "div": 0.155, "clade_membership": { @@ -60350,28 +60621,37 @@ "branch_attrs": { "mutations": { "nuc": [ - "C741T", - "T4526C", - "C4934T", - "A5424C", - "C11201T" + "C4653T", + "T5716A", + "A6587G", + "C6683T", + "A6933G", + "G7973A", + "A8048G", + "G10004A", + "C12664T", + "G13196T" ], - "F": [ - "I492T" + "G": [ + "E114G", + "S146L" ], - "M2-2": [ - "E59D" + "L": [ + "S1833L" + ], + "SH": [ + "S75T" ] }, "labels": { - "aa": "F: I492T; M2-2: E59D" + "aa": "G: E114G, S146L; L: S1833L; SH: S75T" } } }, { - "name": "PP947661", + "name": "PP947612", "node_attrs": { - "div": 0.156, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -60379,117 +60659,30 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1892A", - "G3813A", - "A5518C", - "G6835A", - "C6836T", - "G7694A", - "A8468G" - ], - "G": [ - "A197I" + "C814T", + "A858G", + "A861G", + "C4174T", + "G4506A", + "A5001G", + "T6426C", + "C8813T", + "A10376G", + "G13193A" ], - "SH": [ - "N9H" + "M2-1": [ + "I89V" ] }, "labels": { - "aa": "G: A197I; SH: N9H" + "aa": "M2-1: I89V" } } } ] - } - ] - } - ] - }, - { - "name": "NODE_0000537", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T285C", - "G1451A", - "G3009A", - "A3636G", - "A4290G", - "A6148G", - "G11336A", - "C11492T", - "G11495A", - "C12704T" - ] - } - }, - "children": [ - { - "name": "NODE_0000538", - "node_attrs": { - "div": 0.152, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "MZ851993", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A171T", - "C563T", - "G2556T", - "G2981A", - "G3564A", - "C3609T", - "-4692G", - "-4693T", - "A4720-", - "T4721-", - "C4745T", - "A5631G", - "C6000T", - "C7144T", - "A9122G", - "G10498A", - "G11900A", - "G12779A", - "C13332T" - ], - "L": [ - "S1111N" - ], - "M": [ - "S131I" - ], - "N": [ - "T175I" - ] - }, - "labels": { - "aa": "L: S1111N; M: S131I; N: T175I" - } - } }, { - "name": "NODE_0000539", + "name": "NODE_0000541", "node_attrs": { "div": 0.153, "clade_membership": { @@ -60499,21 +60692,19 @@ "branch_attrs": { "mutations": { "nuc": [ - "G5793A", - "C5972T", - "C7096T" + "C6849A" ], - "SH": [ - "T160I" + "G": [ + "N201K" ] }, "labels": { - "aa": "SH: T160I" + "aa": "G: N201K" } }, "children": [ { - "name": "NODE_0000540", + "name": "NODE_0000542", "node_attrs": { "div": 0.154, "clade_membership": { @@ -60523,42 +60714,41 @@ "branch_attrs": { "mutations": { "nuc": [ - "T2428C", - "A4380G", - "G4496A", - "T5075C", - "C6068T", - "C6767T", - "G6994A", - "T7103C", - "T7109C", - "T7131C", - "T7135C", - "G7136A", - "A7262G", - "C7490T", - "T10217C", - "A10322G", - "G11840A", - "G12863A", - "C12987T" - ], - "F": [ - "S482N" + "G313A", + "A726G", + "A732G", + "T1218C", + "T1382A", + "G1397A", + "A5355T", + "C6666T", + "C6881T", + "G7066A", + "T7328C", + "T8522C", + "C8921T", + "G9131A", + "C9765T" ], "G": [ - "P172S" + "A212V" + ], + "M2-2": [ + "K36N" + ], + "N": [ + "A92T" ] }, "labels": { - "aa": "F: S482N; G: P172S" + "aa": "G: A212V; M2-2: K36N; N: A92T" } }, "children": [ { - "name": "PP947651", + "name": "PP947642", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -60566,92 +60756,45 @@ "branch_attrs": { "mutations": { "nuc": [ - "C4653T", - "T5716A", - "A6587G", - "C6683T", - "A6933G", - "G7973A", - "A8048G", - "G10004A", - "C12664T", - "G13196T" + "A1385G", + "C1847T", + "C2372T", + "T4053C", + "G4095A", + "C4230T", + "G4290A", + "T4443C", + "C4578T", + "T6682C", + "T6711C", + "A6721G", + "T6807C", + "T7064C", + "C7628T", + "A8367G", + "G8996A", + "C10187T", + "T11174C", + "T11535C", + "C12611T" ], "G": [ - "E114G", - "S146L" + "S146P", + "R159G" ], "L": [ - "S1833L" - ], - "SH": [ - "S75T" - ] - }, - "labels": { - "aa": "G: E114G, S146L; L: S1833L; SH: S75T" - } - } - }, - { - "name": "PP947612", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C814T", - "A858G", - "A861G", - "C4174T", - "G4506A", - "A5001G", - "T6426C", - "C8813T", - "A10376G", - "G13193A" - ], - "M2-1": [ - "I89V" + "I401V" ] }, "labels": { - "aa": "M2-1: I89V" + "aa": "G: S146P, R159G; L: I401V" } } - } - ] - }, - { - "name": "NODE_0000541", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C6849A" - ], - "G": [ - "N201K" - ] }, - "labels": { - "aa": "G: N201K" - } - }, - "children": [ { - "name": "NODE_0000542", + "name": "NODE_0000543", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -60659,41 +60802,27 @@ "branch_attrs": { "mutations": { "nuc": [ - "G313A", - "A726G", - "A732G", - "T1218C", - "T1382A", - "G1397A", - "A5355T", - "C6666T", - "C6881T", - "G7066A", - "T7328C", - "T8522C", - "C8921T", - "G9131A", - "C9765T" - ], - "G": [ - "A212V" + "G1476A", + "A3789G", + "G6151A", + "C6782T", + "T7058C", + "G9347A", + "G11900A" ], - "M2-2": [ - "K36N" - ], - "N": [ - "A92T" + "P": [ + "A77T" ] }, "labels": { - "aa": "G: A212V; M2-2: K36N; N: A92T" + "aa": "P: A77T" } }, "children": [ { - "name": "PP947642", + "name": "PP947643", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -60701,45 +60830,46 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1385G", - "C1847T", - "C2372T", - "T4053C", - "G4095A", - "C4230T", - "G4290A", - "T4443C", - "C4578T", - "T6682C", - "T6711C", - "A6721G", - "T6807C", - "T7064C", - "C7628T", - "A8367G", - "G8996A", - "C10187T", - "T11174C", - "T11535C", - "C12611T" + "C300A", + "A1669G", + "G3810A", + "A5666C", + "G6274A", + "T6342C", + "G6835A", + "G6982A", + "C7002T", + "C7106T", + "G7137A", + "G7438A", + "A10718G", + "C11111T", + "G11630A", + "A12197G" ], "G": [ - "S146P", - "R159G" + "A10T", + "A197T" ], "L": [ - "I401V" + "S91N" + ], + "P": [ + "K141R" + ], + "SH": [ + "N58T" ] }, "labels": { - "aa": "G: S146P, R159G; L: I401V" + "aa": "G: A10T, A197T; L: S91N; P: K141R; SH: N58T" } } }, { - "name": "NODE_0000543", + "name": "PP947613", "node_attrs": { - "div": 0.154, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -60747,119 +60877,67 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1476A", - "A3789G", - "G6151A", - "C6782T", - "T7058C", - "G9347A", - "G11900A" + "G876A", + "C973T", + "A2683G", + "-6224T", + "C6225A", + "A6228-", + "C6572T", + "C6625A", + "G6822A", + "T7037C", + "T7089C", + "C7092T", + "A7253G", + "A11735G", + "C12224T", + "C12392T", + "A12950G", + "T13040C" ], - "P": [ - "A77T" + "G": [ + "S109L", + "L127M", + "N152T" ] }, "labels": { - "aa": "P: A77T" - } - }, - "children": [ - { - "name": "PP947643", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C300A", - "A1669G", - "G3810A", - "A5666C", - "G6274A", - "T6342C", - "G6835A", - "G6982A", - "C7002T", - "C7106T", - "G7137A", - "G7438A", - "A10718G", - "C11111T", - "G11630A", - "A12197G" - ], - "G": [ - "A10T", - "A197T" - ], - "L": [ - "S91N" - ], - "P": [ - "K141R" - ], - "SH": [ - "N58T" - ] - }, - "labels": { - "aa": "G: A10T, A197T; L: S91N; P: K141R; SH: N58T" - } - } - }, - { - "name": "PP947613", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G876A", - "C973T", - "A2683G", - "-6224T", - "C6225A", - "A6228-", - "C6572T", - "C6625A", - "G6822A", - "T7037C", - "T7089C", - "C7092T", - "A7253G", - "A11735G", - "C12224T", - "C12392T", - "A12950G", - "T13040C" - ], - "G": [ - "S109L", - "L127M", - "N152T" - ] - }, - "labels": { - "aa": "G: S109L, L127M, N152T" - } - } + "aa": "G: S109L, L127M, N152T" } - ] + } } ] + } + ] + }, + { + "name": "NODE_0000544", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G5974A", + "A11126C" + ], + "SH": [ + "V161I" + ] }, + "labels": { + "aa": "SH: V161I" + } + }, + "children": [ { - "name": "NODE_0000544", + "name": "PP947628", "node_attrs": { - "div": 0.153, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -60867,22 +60945,120 @@ "branch_attrs": { "mutations": { "nuc": [ - "G5974A", - "A11126C" + "C735T", + "T1047C", + "T1560A", + "C1607T", + "C1760T", + "G3150A", + "G4038A", + "C4192T", + "C4961T", + "A5538T", + "C5747T", + 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+ ], + "L": [ + "S895T" + ], + "P": [ + "L64P", + "V82A", + "K227R" ] }, "labels": { - "aa": "SH: V161I" + "aa": "G: P172S; L: S895T; P: L64P, V82A, K227R" } }, "children": [ { - "name": "PP947628", + "name": "NODE_0000546", "node_attrs": { - "div": 0.155, + "div": 0.159, "clade_membership": { "value": "A2b2" } @@ -60890,120 +61066,168 @@ "branch_attrs": { "mutations": { "nuc": [ - "C735T", - "T1047C", - "T1560A", - "C1607T", - "C1760T", - "G3150A", - "G4038A", - "C4192T", - "C4961T", - "A5538T", - "C5747T", - "A5766G", - "G5800A", - "C5916T", - "C6136T", - "C6733T", - "G6800A", - "G6822A", - "G6826T", - "G6879A", - "A6987G", - "A7007G", + "T309C", + "A359G", + "T1794C", + "A2072C", + "G2300A", + "C2327T", + "G2758A", + "G2857A", + "T2943C", + "C2946T", + "A3285C", + "T4563C", + "A5553G", + "G5780A", + "T5807C", + "A5943C", + "G5962A", + "A5976G", + "T6129C", + "C6455T", + "C6551T", + "A6966-", + "T6967C", + "G6968A", + "C6972-", + "A6973-", + "G6974-", + "C6975-", + "T6976-", + 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"branch_attrs": { - "mutations": { - "nuc": [ - "C6967-", - "A6968-", - "A6969-", - "A6970-", - "A6971-" - ] - } - } - } - ] + } } ] } ] + } + ] + }, + { + "name": "NODE_0000550", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A4473G", + "G10859A", + "T11897C", + "A13342T" + ] + } + }, + "children": [ + { + "name": "PQ074242", + "node_attrs": { + "div": 0.161, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G282A", + "A344G", + "G492A", + "A576G", + "C624T", + "A663G", + "A1092G", + "A1146G", + "T1520C", + "G1571A", + "T1594C", + "A2072G", + "G2626A", + "C2689T", + "G2857A", + "C3100A", + "G3204A", + "G3813A", + "G3909A", + "A4572G", + "T4683-", + "A4684-", + "A4685-", + "A4686-", + "A4687-", + "C4688-", + "A4689-", + "A4690-", + "A4691-", + "-4710A", + "-4711T", + "-4712A", + "-4713A", + "-4714A", + "-4715A", + "-4716T", + "-4717A", + "-4718A", 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P: L116S; SH: R116K, V155F" + } + } }, { - "name": "NODE_0000550", + "name": "NODE_0000551", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -61276,17 +61485,18 @@ "branch_attrs": { "mutations": { "nuc": [ - "A4473G", - "G10859A", - "T11897C" + "C6898-", + "T7100C", + "T9836C", + "G10103A" ] } }, "children": [ { - "name": "PQ074242", + "name": "NODE_0000552", "node_attrs": { - "div": 0.161, + "div": 0.159, "clade_membership": { "value": "A2b2" } @@ -61294,134 +61504,155 @@ "branch_attrs": { "mutations": { "nuc": [ - "G282A", - "A344G", - "G492A", - "A576G", - "C624T", - "A663G", - "A1092G", - "A1146G", - "T1520C", - "G1571A", - "T1594C", - "A2072G", - "G2626A", - "C2689T", - "G2857A", - "C3100A", - "G3204A", - "G3813A", - "G3909A", - "A4572G", - "T4683-", - "A4684-", - "A4685-", - "A4686-", - "A4687-", - "C4688-", - "A4689-", - "A4690-", - "A4691-", - "-4710A", - "-4711T", - "-4712A", - "-4713A", - "-4714A", - "-4715A", - "-4716T", - "-4717A", 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] + }, + "labels": { + "aa": "P: K260N, I261F" + } + } + }, + { + "name": "PQ117893", + "node_attrs": { + "div": 0.16, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G117A", + "C148T", + "T1206C", + "A1364T", + "C2392T", + "T3568C", + "C3621T", + "T3624C", + "T3638A", + "G4152A", + "G5391A", + "G5575A", + "A5697G", + "C6683T", + "A6933T", + "C7078T", + "G7457A", + "T8907C", + "T9653C", + "A10277G", + "C10514T", + "A12002G" + ], + "F": [ + "F196Y" + ], + "G": [ + "S146L" + ], + "N": [ + "P37S" + ], + "SH": [ + "G28S" + ] + }, + "labels": { + "aa": "F: F196Y; G: S146L; N: P37S; SH: G28S" + } + } + } + ] }, { - "name": "NODE_0000551", + "name": "NODE_0000553", "node_attrs": { - "div": 0.155, + "div": 0.157, "clade_membership": { "value": "A2b2" } @@ -61429,17 +61660,42 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6898-", - "T7100C", - "T9836C", - "G10103A", - "A13342T" + "C666T", + "G3513A", + "G4152A", + "C4557A", + "G5959A", + "C6000T", + "A6375G", + "A6492C", + "C6507T", + "-6898A", + "C8264T", + "A8708T", + "T11339C", + "C11862T", + "T12182C", + "T12215C", + "T12611C", + "C12623T" + ], + "G": [ + "I43M", + "R159K", + "F162L", + "Q218K" + ], + "SH": [ + "E156K" ] + }, + "labels": { + "aa": "G: I43M, R159K, F162L, Q218K; SH: E156K" } }, "children": [ { - "name": "NODE_0000552", + "name": "NODE_0000554", "node_attrs": { "div": 0.158, "clade_membership": { @@ -61449,67 +61705,24 @@ "branch_attrs": { "mutations": { "nuc": [ - "A726G", - "T2956C", - "C2957T", - "G2972A", - "G3015A", - "T3705C", - "A4455G", - "G4796A", - "C5724T", - "G6083A", - "T6202C", - "C6456A", - "A6674C", - "G6695C", - "T6711C", - "C6730T", - "C6760T", - "C6777T", - "G6790A", - "C6836T", - "A6855G", - "A6895-", - "T6896-", - "G6897-", - "A6899-", - "A6900-", - "A6902T", - "A6903G", - "T6904C", - "G6906A", - "-6907A", - "-6908A", - "-6909G", - "-6910T", - "-6911A", - "-6912G", - "C7054A", - "C7106T", - "A7289G", - "T7455C", - "G7892A", - "G8435A", - "T10670C", - "A10844T", - "A11147G" + "G6750A", + "T9341C", + "C11682T", + "G13208A" ], - "G": [ - "R150T", - "A182T", - "A197V" + "L": [ + "P1506S" ] }, "labels": { - "aa": "G: R150T, A182T, A197V" + "aa": "L: P1506S" } }, "children": [ { - "name": "PQ117894", + "name": "PQ117895", "node_attrs": { - "div": 0.159, + "div": 0.16, "clade_membership": { "value": "A2b2" } @@ -61517,87 +61730,139 @@ "branch_attrs": { "mutations": { "nuc": [ - "A2027T", - "A2028T", - "A2145G", - "A2951T", - "C9206A", - "A9809T", - "C10688T", - "A11051G", - "C11183T", - "G11669A", - "A12383G", - "T12527C" + "A72G", + "G99A", + "C585T", + "T1994C", + "C2085T", + "C2893T", + "T2975C", + "C3837T", + "C3849T", + "G4023A", + "G5583A", + "A5984G", + "G6069A", + "A6182C", + "T6300C", + "G6337A", + "T6342C", + "C6348A", + "T6363C", + "T6366C", + "C6464A", + "T6489C", + "T6711C", + "C6760T", + "G6783A", + "C7358T", + "T8261G", + "C8921T", + "T8957C", + "A10030G", + "A10553G", + "T10919C", + "C11234T", + "C11779T", + "C13049T", + "C13224A", + "A13252G" + ], + "G": [ + "A31T", + "S73Y", + "K159R" ], - "P": [ - "K260N", - "I261F" + "L": [ + "N955S", + "S1538L" + ], + "SH": [ + "H164R" ] }, "labels": { - "aa": "P: K260N, I261F" + "aa": "G: A31T, S73Y, K159R; L: N955S, S1538L; SH: H164R" } } }, { - "name": "PQ117893", + "name": "PP716095", "node_attrs": { "div": 0.16, + "accession": "PP716095", + "author": { + "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", + "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." + }, "clade_membership": { "value": "A2b2" + }, + "region": { + "value": "Europe" + }, + "country": { + "value": "Russia" } }, "branch_attrs": { "mutations": { "nuc": [ - "G117A", - "C148T", - "T1206C", - "A1364T", - "C2392T", - "T3568C", - "C3621T", - "T3624C", - "T3638A", - "G4152A", - "G5391A", - "G5575A", - "A5697G", - "C6683T", - "A6933T", - "C7078T", - "G7457A", - "T8907C", - "T9653C", - "A10277G", - "C10514T", - "A12002G" - ], - "F": [ - "F196Y" + "C24A", + "T213C", + "A1265G", + "T1452C", + "T2513C", + "A3018G", + "T3405A", + "G3894A", + "G4257A", + "C4750T", + "T4991C", + "A5563C", + "A5831G", + "C5994T", + "G6722A", + "G7401A", + "G7463A", + "A7574G", + "A7703G", + "A8951G", + "C9524T", + "T10007C", + "A10865G", + "A11138G", + "A11144G", + "A11162G", + "G11774A", + "A11918G", + "T13241G" ], "G": [ - "S146L" + "S172P" + ], + "L": [ + "V79I" ], - "N": [ - "P37S" + "M2-1": [ + "A5V" ], "SH": [ - "G28S" + "K24Q", + "K113R" ] }, "labels": { - "aa": "F: F196Y; G: S146L; N: P37S; SH: G28S" + "aa": "G: S172P; L: V79I; M2-1: A5V; SH: K24Q, K113R" } } } ] }, { - "name": "NODE_0000553", + "name": "NODE_0000555", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -61605,44 +61870,28 @@ "branch_attrs": { "mutations": { "nuc": [ - "C666T", - "G3513A", - "G4152A", - "C4557A", - "G5959A", - "C6000T", - "A6375G", - "A6492C", - "C6507T", - "-6898A", - "C8264T", - "A8708T", - "T11339C", - "C11862T", - "T12182C", - "T12215C", - "T12611C", - "C12623T" + "C6602T", + "T6843C", + "T6896C", + "A7153G", + "C10514T", + "T11009C", + "C12126T" ], "G": [ - "I43M", - "R159K", - "F162L", - "Q218K" - ], - "SH": [ - "E156K" + "S119L", + "M217T" ] }, "labels": { - "aa": "G: I43M, R159K, F162L, Q218K; SH: E156K" + "aa": "G: S119L, M217T" } }, "children": [ { - "name": "NODE_0000554", + "name": "NODE_0000556", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -61650,102 +61899,100 @@ "branch_attrs": { "mutations": { "nuc": [ - "G6750A", - "T9341C", - "C11682T", - "G13208A" + "G6722A", + "C7076T" ], - "L": [ - "P1506S" + "G": [ + "S172P" ] }, "labels": { - "aa": "L: P1506S" + "aa": "G: S172P" } }, "children": [ { - "name": "PQ117895", + "name": "PP716096", "node_attrs": { "div": 0.16, + "accession": "PP716096", + "author": { + "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", + "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." + }, "clade_membership": { "value": "A2b2" + }, + "region": { + "value": "Europe" + }, + "country": { + "value": "Russia" } }, "branch_attrs": { "mutations": { "nuc": [ - "A72G", - "G99A", - "C585T", - "T1994C", - "C2085T", - "C2893T", - "T2975C", - "C3837T", - "C3849T", - "G4023A", - "G5583A", - "A5984G", - "G6069A", - "A6182C", - "T6300C", - "G6337A", - "T6342C", - "C6348A", - "T6363C", - "T6366C", - "C6464A", - "T6489C", - "T6711C", - "C6760T", - "G6783A", - "C7358T", - "T8261G", - "C8921T", - "T8957C", - "A10030G", - "A10553G", - "T10919C", - "C11234T", - "C11779T", - "C13049T", - "C13224A", - "A13252G" + "C78T", + "T201C", + "A1062G", + "A1844G", + "A2048T", + "G3168A", + "G3171A", + "C4284T", + "T4979C", + "A5159G", + "G5271A", + "A5283G", + "T5392A", + "G5956T", + "G6565A", + "C6777T", + "T6950A", + "G7044A", + "C7144T", + "G8333A", + "A8387G", + "G8543A", + "A8831G", + "A9419G", + "A9914G", + "T9926A", + "A10171G", + "G10491A", + "T11792C", + "T12653C", + "C12824A", + "C13119T" ], "G": [ - "A31T", - "S73Y", - "K159R" + "A107T" ], "L": [ - "N955S", - "S1538L" + "N1002S", + "V1109I" + ], + "M2-1": [ + "D179N", + "T183A" + ], + "M2-2": [ + "S49T" ], "SH": [ - "H164R" + "V155F" ] }, "labels": { - "aa": "G: A31T, S73Y, K159R; L: N955S, S1538L; SH: H164R" + "aa": "G: A107T; L: N1002S, V1109I; M2-1: D179N, T183A; M2-2: S49T; SH: V155F" } } }, { - "name": "PP716095", + "name": "NODE_0000557", "node_attrs": { - "div": 0.159, - "accession": "PP716095", - "author": { - "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", - "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." - }, - "country": { - "value": "Russia" - }, - "region": { - "value": "Europe" - }, + "div": 0.161, "clade_membership": { "value": "A2b2" } @@ -61754,60 +62001,110 @@ "mutations": { "nuc": [ "C24A", - "T213C", - "A1265G", - "T1452C", - "T2513C", - "A3018G", - "T3405A", - "G3894A", - "G4257A", - "C4750T", - "T4991C", - "A5563C", - "A5831G", - "C5994T", - "G6722A", - "G7401A", - "G7463A", - "A7574G", - "A7703G", - "A8951G", - "C9524T", - "T10007C", - "A10865G", - "A11138G", - "A11144G", - "A11162G", - "G11774A", - "A11918G", - "T13241G" + "C753T", + "C1437T", + "C1773T", + "G2102A", + "A2845G", + "G2981A", + "C4492T", + "C5550T", + "A5722G", + "A5937G", + "A5971T", + "C6166T", + "T6299C", + "T6300C", + "T6342C", + "T6463C", + "T6489C", + "C6495T", + "C6773T", + "C6782T", + "T6992C", + "G8408A", + "T8606C", + "T9563C", + "T9566C", + "C10071T", + "T10694C", + "C11456T", + "A11933G", + "G12890A", + "T12956A", + "C13303A" ], "G": [ - "S172P" - ], - "L": [ - "V79I" + "V18A", + "S73P" ], - "M2-1": [ - "A5V" + "P": [ + "P64S" ], "SH": [ - "K24Q", - "K113R" + "T77A", + "I160L" ] }, "labels": { - "aa": "G: S172P; L: V79I; M2-1: A5V; SH: K24Q, K113R" + "aa": "G: V18A, S73P; P: P64S; SH: T77A, I160L" } - } + }, + "children": [ + { + "name": "PP716094", + "node_attrs": { + "div": 0.161, + "accession": "PP716094", + "author": { + "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", + "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." + }, + "clade_membership": { + "value": "A2b2" + }, + "region": { + "value": "Europe" + }, + "country": { + "value": "Russia" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "PP716093", + "node_attrs": { + "div": 0.161, + "accession": "PP716093", + "author": { + "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", + "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." + }, + "clade_membership": { + "value": "A2b2" + }, + "region": { + "value": "Europe" + }, + "country": { + "value": "Russia" + } + }, + "branch_attrs": { + "mutations": {} + } + } + ] } ] }, { - "name": "NODE_0000555", + "name": "NODE_0000558", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -61815,28 +62112,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6602T", - "T6843C", - "T6896C", - "A7153G", - "C10514T", - "T11009C", - "C12126T" - ], - "G": [ - "S119L", - "M217T" + "C6760T" ] - }, - "labels": { - "aa": "G: S119L, M217T" } }, "children": [ { - "name": "NODE_0000556", + "name": "NODE_0000559", "node_attrs": { - "div": 0.157, + "div": 0.159, "clade_membership": { "value": "A2b2" } @@ -61844,212 +62128,51 @@ "branch_attrs": { "mutations": { "nuc": [ - "G6722A", - "C7076T" - ], - "G": [ - "S172P" + "T3405C", + "T6018C", + "C6447T", + "T9614C", + "G10565A", + "G10736A", + "T11000C", + "A11555G", + "A13281T", + "C13283A", + "G13288T" ] - }, - "labels": { - "aa": "G: S172P" } }, "children": [ { - "name": "PP716096", + "name": "OY757785", "node_attrs": { - "div": 0.16, - "accession": "PP716096", - "author": { - "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", - "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." - }, - "country": { - "value": "Russia" - }, - "region": { - "value": "Europe" - }, + "div": 0.159, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C78T", - "T201C", - "A1062G", - "A1844G", - "A2048T", - "G3168A", - "G3171A", - "C4284T", - "T4979C", - "A5159G", - "G5271A", - "A5283G", - "T5392A", - "G5956T", - "G6565A", - "C6777T", - "T6950A", - "G7044A", - "C7144T", - "G8333A", - "A8387G", - "G8543A", - "A8831G", - "A9419G", - "A9914G", - "T9926A", - "A10171G", - "G10491A", - "T11792C", - "T12653C", - "C12824A", - "C13119T" - ], - "G": [ - "A107T" - ], - "L": [ - "N1002S", - "V1109I" - ], - "M2-1": [ - "D179N", - "T183A" - ], - "M2-2": [ - "S49T" - ], - "SH": [ - "V155F" - ] - }, - "labels": { - "aa": "G: A107T; L: N1002S, V1109I; M2-1: D179N, T183A; M2-2: S49T; SH: V155F" - } + "mutations": {} } }, { - "name": "NODE_0000557", + "name": "OY757607", "node_attrs": { - "div": 0.16, + "div": 0.159, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C24A", - "C753T", - "C1437T", - "C1773T", - "G2102A", - "A2845G", - "G2981A", - "C4492T", - "C5550T", - "A5722G", - "A5937G", - "A5971T", - "C6166T", - "T6299C", - "T6300C", - "T6342C", - "T6463C", - "T6489C", - "C6495T", - "C6773T", - "C6782T", - "T6992C", - "G8408A", - "T8606C", - "T9563C", - "T9566C", - "C10071T", - "T10694C", - "C11456T", - "A11933G", - "G12890A", - "T12956A", - "C13303A" - ], - "G": [ - "V18A", - "S73P" - ], - "P": [ - "P64S" - ], - "SH": [ - "T77A", - "I160L" - ] - }, - "labels": { - "aa": "G: V18A, S73P; P: P64S; SH: T77A, I160L" - } - }, - "children": [ - { - "name": "PP716094", - "node_attrs": { - "div": 0.16, - "accession": "PP716094", - "author": { - "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", - "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." - }, - "country": { - "value": "Russia" - }, - "region": { - "value": "Europe" - }, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "PP716093", - "node_attrs": { - "div": 0.16, - "accession": "PP716093", - "author": { - "author": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D.", - "value": "Fadeev,A.,Ivanov,I.,Sukailo,D.,Komissarov,A.,Danilenko,D.,Lioznov,D." - }, - "country": { - "value": "Russia" - }, - "region": { - "value": "Europe" - }, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + "mutations": {} + } } ] }, { - "name": "NODE_0000558", + "name": "NODE_0000560", "node_attrs": { - "div": 0.157, + "div": 0.158, "clade_membership": { "value": "A2b2" } @@ -62057,15 +62180,18 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6760T" + "A1080C", + "A1325G", + "A8057G", + "T13342A" ] } }, "children": [ { - "name": "NODE_0000559", + "name": "PQ117901", "node_attrs": { - "div": 0.158, + "div": 0.161, "clade_membership": { "value": "A2b2" } @@ -62073,51 +62199,72 @@ "branch_attrs": { "mutations": { "nuc": [ - "T3405C", - "T6018C", - "C6447T", - "T9614C", - "G10565A", - "G10736A", - "T11000C", - "A11555G", - "A13281T", - "C13283A", - "G13288T" + "A429G", + "A810T", + "G819A", + "A2080G", + "G3207A", + "C3945T", + "T4074C", + "T4347C", + "G4605A", + "T4875C", + "A5705G", + "C6023T", + "G6075A", + "A6484T", + "C6492T", + "G6722A", + "T6965C", + "T6999C", + "A7012G", + "G7044A", + "G7137A", + "C7452T", + "C7550T", + "G7841A", + "T8120C", + "A8418G", + "G8755A", + "A9224T", + "C9473T", + "T10202C", + "T10653C", + "C10967A", + "A11141G", + "G11840A", + "T12203C", + "C12305T", + "G12326A", + "A12563G", + "T12752A", + "C12755T", + "C13049T" + ], + "G": [ + "I80F" + ], + "L": [ + "I418V", + "R530K" + ], + "P": [ + "K278R" + ], + "SH": [ + "E71G", + "S177L" ] - } - }, - "children": [ - { - "name": "OY757785", - "node_attrs": { - "div": 0.158, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } }, - { - "name": "OY757607", - "node_attrs": { - "div": 0.158, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } + "labels": { + "aa": "G: I80F; L: I418V, R530K; P: K278R; SH: E71G, S177L" } - ] + } }, { - "name": "NODE_0000560", + "name": "NODE_0000561", "node_attrs": { - "div": 0.158, + "div": 0.159, "clade_membership": { "value": "A2b2" } @@ -62125,16 +62272,23 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1080C", - "A1325G", - "A8057G", - "T13342A" + "A2959G", + "G4245A", + "C6500A", + "A10052C" + ], + "G": [ + "P85Q", + "K159R" ] + }, + "labels": { + "aa": "G: P85Q, K159R" } }, "children": [ { - "name": "PQ117901", + "name": "PQ117899", "node_attrs": { "div": 0.161, "clade_membership": { @@ -62144,72 +62298,50 @@ "branch_attrs": { "mutations": { "nuc": [ - "A429G", - "A810T", - "G819A", - "A2080G", - "G3207A", - "C3945T", - "T4074C", - "T4347C", - "G4605A", - "T4875C", - "A5705G", - "C6023T", - "G6075A", - "A6484T", - "C6492T", - "G6722A", - "T6965C", - "T6999C", - "A7012G", - "G7044A", - "G7137A", - "C7452T", - "C7550T", - "G7841A", - "T8120C", - "A8418G", - "G8755A", - "A9224T", - "C9473T", - "T10202C", - "T10653C", - "C10967A", - "A11141G", - "G11840A", - "T12203C", - "C12305T", - "G12326A", - "A12563G", - "T12752A", - "C12755T", - "C13049T" - ], - "G": [ - "I80F" + "G51A", + "A963G", + "C1826T", + "A1895G", + "C2148A", + "C2491T", + "T3498C", + "G4464A", + "T5730C", + "T5750C", + "T6510C", + "T6864C", + "T7037C", + "C7088T", + "A7307G", + "C7806T", + "C8108T", + "A8316G", + "A8531G", + "T9474C", + "A10376G", + "T10379C", + "T10409C", + "G11774A", + "C12995T", + "A13151G", + "A13291T" ], "L": [ - "I418V", - "R530K" - ], - "P": [ - "K278R" + "I384V" ], "SH": [ - "E71G", - "S177L" + "L86P" ] }, "labels": { - "aa": "G: I80F; L: I418V, R530K; P: K278R; SH: E71G, S177L" + "aa": "L: I384V; SH: L86P" } } }, { - "name": "NODE_0000561", + "name": "NODE_0000562", "node_attrs": { - "div": 0.158, + "div": 0.159, "clade_membership": { "value": "A2b2" } @@ -62217,25 +62349,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "A2959G", - "G4245A", - "C6500A", - "A10052C" - ], - "G": [ - "P85Q", - "K159R" + "A8999G" ] - }, - "labels": { - "aa": "G: P85Q, K159R" } }, "children": [ { - "name": "PQ117899", + "name": "PQ117900", "node_attrs": { - "div": 0.16, + "div": 0.161, "clade_membership": { "value": "A2b2" } @@ -62243,50 +62365,56 @@ "branch_attrs": { "mutations": { "nuc": [ - "G51A", - "A963G", - "C1826T", - "A1895G", - "C2148A", - "C2491T", - "T3498C", - "G4464A", - "T5730C", - "T5750C", - "T6510C", - "T6864C", - "T7037C", - "C7088T", - "A7307G", - "C7806T", - "C8108T", - "A8316G", - "A8531G", - "T9474C", - "A10376G", - "T10379C", - "T10409C", - "G11774A", - "C12995T", - "A13151G", - "A13291T" + "A984G", + "T1815C", + "T2605C", + "A2612G", + "T3316C", + "G4023A", + "C4919T", + "T6113G", + "G6114A", + "C6549T", + "G6578A", + "A6620G", + "C6789T", + "C7452T", + "C7766T", + "A8062T", + "G8124A", + "A9074G", + "G9542A", + "A9732C", + "T10069C", + "C10205T", + "C10289T", + "G10565A", + "C11087T", + "G12515A" + ], + "G": [ + "S111N", + "N125S" ], "L": [ - "I384V" + "N299I", + "V320I", + "I856L", + "L968S" ], - "SH": [ - "L86P" + "M": [ + "M150V" ] }, "labels": { - "aa": "L: I384V; SH: L86P" + "aa": "G: S111N, N125S; L: N299I, V320I, I856L, L968S; M: M150V" } } }, { - "name": "NODE_0000562", + "name": "NODE_0000563", "node_attrs": { - "div": 0.158, + "div": 0.16, "clade_membership": { "value": "A2b2" } @@ -62294,13 +62422,29 @@ "branch_attrs": { "mutations": { "nuc": [ - "A8999G" + "C1568T", + "T3078C", + "A3987G", + "C5614T", + "C6195A", + "C6487T", + "T7122C", + "G8057A", + "G9989A", + "T10550C", + "C12932T" + ], + "G": [ + "P81S" ] + }, + "labels": { + "aa": "G: P81S" } }, "children": [ { - "name": "PQ117900", + "name": "PP944383", "node_attrs": { "div": 0.16, "clade_membership": { @@ -62308,111 +62452,20 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A984G", - "T1815C", - "T2605C", - "A2612G", - "T3316C", - "G4023A", - "C4919T", - "T6113G", - "G6114A", - "C6549T", - "G6578A", - "A6620G", - "C6789T", - "C7452T", - "C7766T", - "A8062T", - "G8124A", - "A9074G", - "G9542A", - "A9732C", - "T10069C", - "C10205T", - "C10289T", - "G10565A", - "C11087T", - "G12515A" - ], - "G": [ - "S111N", - "N125S" - ], - "L": [ - "N299I", - "V320I", - "I856L", - "L968S" - ], - "M": [ - "M150V" - ] - }, - "labels": { - "aa": "G: S111N, N125S; L: N299I, V320I, I856L, L968S; M: M150V" - } + "mutations": {} } }, { - "name": "NODE_0000563", + "name": "PP944382", "node_attrs": { - "div": 0.159, + "div": 0.16, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C1568T", - "T3078C", - "A3987G", - "C5614T", - "C6195A", - "C6487T", - "T7122C", - "G8057A", - "G9989A", - "T10550C", - "C12932T" - ], - "G": [ - "P81S" - ] - }, - "labels": { - "aa": "G: P81S" - } - }, - "children": [ - { - "name": "PP944383", - "node_attrs": { - "div": 0.159, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "PP944382", - "node_attrs": { - "div": 0.159, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - } - ] + "mutations": {} + } } ] } @@ -62439,11 +62492,29 @@ ] } ] - }, + } + ] + }, + { + "name": "NODE_0000564", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A1484G" + ] + } + }, + "children": [ { - "name": "NODE_0000564", + "name": "NODE_0000565", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } @@ -62451,15 +62522,80 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1484G" + "G6968A" ] } }, "children": [ { - "name": "NODE_0000565", + "name": "PP947666", "node_attrs": { - "div": 0.152, + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C603T", + "A702G", + "G939A", + "C1038A", + "C1078T", + "C2318T", + "C3531T", + "G4431A", + "C4745T", + "A5159G", + "A5411G", + "G5448A", + "A5766T", + "T5875C", + "G6001A", + "T6056C", + "T6206G", + "G6627A", + "A6681T", + "G6790A", + "A6933T", + "A7116G", + "G7631A", + "A8558T", + "T9002G", + "A10697G", + "A10892G", + "C11087T", + "G11777A", + "C12518T", + "C12599T", + "T12705A", + "A12791T", + "C13049T" + ], + "G": [ + "A182T" + ], + "L": [ + "E464D", + "S1847T" + ], + "M2-2": [ + "N55S" + ], + "SH": [ + "E170K" + ] + }, + "labels": { + "aa": "G: A182T; L: E464D, S1847T; M2-2: N55S; SH: E170K" + } + } + }, + { + "name": "NODE_0000566", + "node_attrs": { + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -62467,13 +62603,57 @@ "branch_attrs": { "mutations": { "nuc": [ - "G6968A" + "G1233A", + "A1346G", + "T2060C", + "T2203C", + "C2722T", + "A3030G", + "T3108C", + "A5086G", + "T5928C", + "T6213C", + "T6489C", + "C6512T", + "T6635C", + "T6711C", + "C6720T", + "T6731C", + "G6826A", + "G6841A", + "G6939A", + "T6940C", + "T6965A", + "T7089C", + "T7172C", + "C7851A", + "G8765A", + "A9455G", + "G10720A", + "G11858A", + "C13085T" + ], + "G": [ + "P89L", + "V130A", + "D194N", + "A199T" + ], + "L": [ + "L229M", + "S1185N" + ], + "M2-1": [ + "K117R" ] + }, + "labels": { + "aa": "G: P89L, V130A, D194N, A199T; L: L229M, S1185N; M2-1: K117R" } }, "children": [ { - "name": "PP947666", + "name": "PP947665", "node_attrs": { "div": 0.155, "clade_membership": { @@ -62483,62 +62663,20 @@ "branch_attrs": { "mutations": { "nuc": [ - "C603T", - "A702G", - "G939A", - "C1038A", - "C1078T", - "C2318T", - "C3531T", - "G4431A", - "C4745T", - "A5159G", - "A5411G", - "G5448A", - "A5766T", - "T5875C", - "G6001A", - "T6056C", - "T6206G", - "G6627A", - "A6681T", - "G6790A", - "A6933T", - "A7116G", - "G7631A", - "A8558T", - "T9002G", - "A10697G", - "A10892G", - "C11087T", - "G11777A", - "C12518T", - "C12599T", - "T12705A", - "A12791T", - "C13049T" - ], - "G": [ - "A182T" + "A1916G", + "C9119T" ], - "L": [ - "E464D", - "S1847T" - ], - "M2-2": [ - "N55S" - ], - "SH": [ - "E170K" + "P": [ + "I223M" ] }, "labels": { - "aa": "G: A182T; L: E464D, S1847T; M2-2: N55S; SH: E170K" + "aa": "P: I223M" } } }, { - "name": "NODE_0000566", + "name": "PP947575", "node_attrs": { "div": 0.155, "clade_membership": { @@ -62548,114 +62686,110 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1233A", - "A1346G", - "T2060C", - "T2203C", - "C2722T", - "A3030G", - "T3108C", - "A5086G", - "T5928C", - "T6213C", - "T6489C", - "C6512T", - "T6635C", - "T6711C", - "C6720T", - "T6731C", - "G6826A", - "G6841A", - "G6939A", - "T6940C", - "T6965A", - "T7089C", - "T7172C", - "C7851A", - "G8765A", - "A9455G", - "G10720A", - "G11858A", - "C13085T" - ], - "G": [ - "P89L", - "V130A", - "D194N", - "A199T" - ], - "L": [ - "L229M", - "S1185N" - ], - "M2-1": [ - "K117R" + "C4314T" ] - }, - "labels": { - "aa": "G: P89L, V130A, D194N, A199T; L: L229M, S1185N; M2-1: K117R" - } - }, - "children": [ - { - "name": "PP947665", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A1916G", - "C9119T" - ], - "P": [ - "I223M" - ] - }, - "labels": { - "aa": "P: I223M" - } - } - }, - { - "name": "PP947575", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C4314T" - ] - } - } } - ] + } } ] + } + ] + }, + { + "name": "NODE_0000567", + "node_attrs": { + "div": 0.153, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ + { + "name": "OP904126", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C2148-", + "C3561T", + "A4071G", + "A4323G", + "C4745A", + "A5159G", + "C5543T", + "T6575C", + "T6583C", + "T6626C", + "T6730C", + "T6807C", + "T7220C", + "T7235C", + "T7280C", + "T7938A", + "A8714G", + "G9815A", + "C9872T", + "T11307C", + "C12392A" + ], + "G": [ + "V110A", + "S113P", + "L127P", + "F162L" + ], + "L": [ + "L258I" + ], + "SH": [ + "T17I" + ] + }, + "labels": { + "aa": "G: V110A, S113P, L127P, F162L; L: L258I; SH: T17I" + } + } }, { - "name": "NODE_0000567", + "name": "NODE_0000568", "node_attrs": { - "div": 0.152, + "div": 0.153, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "A5361T", + "T5623C", + "A6276C", + "A12236G" + ], + "M2-2": [ + "L38F" + ], + "SH": [ + "F44L" + ] + }, + "labels": { + "aa": "M2-2: L38F; SH: F44L" + } }, "children": [ { - "name": "OP904126", + "name": "NODE_0000569", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -62663,50 +62797,143 @@ "branch_attrs": { "mutations": { "nuc": [ - "C2148-", - "C3561T", - "A4071G", - "A4323G", - "C4745A", - "A5159G", - "C5543T", - "T6575C", - "T6583C", - "T6626C", - "T6730C", - "T6807C", - "T7220C", - "T7235C", - "T7280C", - "T7938A", - "A8714G", - "G9815A", - "C9872T", - "T11307C", - "C12392A" + "G693C", + "T982C", + "T1555C", + "A1700T", + "C2946T", + "T4683-", + "A4684-", + "A4685-", + "A4686-", + "A4687-", + "C4688-", + "A4689-", + "A4690-", + "A4691-", + "-4710A", + "-4711T", + "-4712A", + "-4713A", + "-4714A", + "-4715A", + "-4716C", + "-4717A", + "-4718A", + "-4719A", + "T5397C", + "C5822A", + "C6146T", + "C6581T", + "G6835A", + "G7082A", + "G7085T", + "A7086T", + "A7087C", + "T7090C", + "C7628T", + "A8267G", + "G8811A", + "G9885A", + "C9995T", + "T11906C", + "A13308T" ], "G": [ - "V110A", - "S113P", - "L127P", - "F162L" + "P112L", + "A197T" ], "L": [ - "L258I" + "V549I", + "E907K" + ], + "P": [ + "L103P", + "E151D" ], "SH": [ - "T17I" + "T110K" ] }, "labels": { - "aa": "G: V110A, S113P, L127P, F162L; L: L258I; SH: T17I" + "aa": "G: P112L, A197T; L: V549I, E907K; P: L103P, E151D; SH: T110K" } - } + }, + "children": [ + { + "name": "PP947693", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "NODE_0000570", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ + { + "name": "PP947660", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T451C", + "T474C", + "A2092G" + ], + "P": [ + "D282G" + ] + }, + "labels": { + "aa": "P: D282G" + } + } + }, + { + "name": "PP947553", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A23C", + "C24-", + "G4940T" + ] + } + } + } + ] + } + ] }, { - "name": "NODE_0000568", + "name": "NODE_0000571", "node_attrs": { - "div": 0.153, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -62714,27 +62941,26 @@ "branch_attrs": { "mutations": { "nuc": [ - "A5361T", - "T5623C", - "A6276C", - "A12236G" - ], - "M2-2": [ - "L38F" + "T5611C", + "C5852T", + "T6807C", + "G7871A", + "T9866C", + "T13088C" ], "SH": [ - "F44L" + "T120I" ] }, "labels": { - "aa": "M2-2: L38F; SH: F44L" + "aa": "SH: T120I" } }, "children": [ { - "name": "NODE_0000569", + "name": "NODE_0000572", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -62742,95 +62968,59 @@ "branch_attrs": { "mutations": { "nuc": [ - "G693C", - "T982C", - "T1555C", - "A1700T", - "C2946T", - "T4683-", - "A4684-", - "A4685-", - "A4686-", - "A4687-", - "C4688-", - "A4689-", - "A4690-", - "A4691-", - "-4710A", - "-4711T", - "-4712A", - "-4713A", - "-4714A", - "-4715A", - "-4716C", - "-4717A", - "-4718A", - "-4719A", - "T5397C", - "C5822A", - "C6146T", - "C6581T", - "G6835A", - "G7082A", - "G7085T", + "T1452C", + "T2086C", + "A3495G", + "G4512A", + "T5253C", + "T5750C", + "T5868C", + "G6790A", "A7086T", "A7087C", "T7090C", - "C7628T", - "A8267G", - "G8811A", - "G9885A", - "C9995T", - "T11906C", - "A13308T" + "C8427T", + "T9474C", + "G9644A", + "T10097C", + "T12638C" ], "G": [ - "P112L", - "A197T" + "A182T" ], - "L": [ - "V549I", - "E907K" + "M2-1": [ + "S173P" ], "P": [ - "L103P", - "E151D" + "L280P" ], "SH": [ - "T110K" + "L86P" ] }, "labels": { - "aa": "G: P112L, A197T; L: V549I, E907K; P: L103P, E151D; SH: T110K" + "aa": "G: A182T; M2-1: S173P; P: L280P; SH: L86P" } }, "children": [ { - "name": "PP947693", + "name": "NODE_0000573", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} - } - }, - { - "name": "NODE_0000570", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" + "mutations": { + "nuc": [ + "C6086T" + ] } }, - "branch_attrs": { - "mutations": {} - }, "children": [ { - "name": "PP947660", + "name": "PP947674", "node_attrs": { "div": 0.155, "clade_membership": { @@ -62838,25 +63028,13 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T451C", - "T474C", - "A2092G" - ], - "P": [ - "D282G" - ] - }, - "labels": { - "aa": "P: D282G" - } + "mutations": {} } }, { - "name": "PP947553", + "name": "PP947557", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -62864,94 +63042,49 @@ "branch_attrs": { "mutations": { "nuc": [ - "A23C", - "C24-", - "G4940T" + "T7058C", + "T7063C", + "T7109C", + "T7122C" ] } } } ] - } - ] - }, - { - "name": "NODE_0000571", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T5611C", - "C5852T", - "T6807C", - "G7871A", - "T9866C", - "T13088C" - ], - "SH": [ - "T120I" - ] }, - "labels": { - "aa": "SH: T120I" - } - }, - "children": [ { - "name": "NODE_0000572", + "name": "NODE_0000574", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T1452C", - "T2086C", - "A3495G", - "G4512A", - "T5253C", - "T5750C", - "T5868C", - "G6790A", - "A7086T", - "A7087C", - "T7090C", - "C8427T", - "T9474C", - "G9644A", - "T10097C", - "T12638C" - ], - "G": [ - "A182T" - ], - "M2-1": [ - "S173P" - ], - "P": [ - "L280P" - ], - "SH": [ - "L86P" - ] - }, - "labels": { - "aa": "G: A182T; M2-1: S173P; P: L280P; SH: L86P" - } + "mutations": {} }, "children": [ { - "name": "NODE_0000573", + "name": "PP947597", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T8009C", + "A8714G" + ] + } + } + }, + { + "name": "NODE_0000575", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -62959,25 +63092,13 @@ "branch_attrs": { "mutations": { "nuc": [ - "C6086T" + "T7785C" ] } }, "children": [ { - "name": "PP947674", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "PP947557", + "name": "NODE_0000576", "node_attrs": { "div": 0.155, "clade_membership": { @@ -62987,65 +63108,67 @@ "branch_attrs": { "mutations": { "nuc": [ - "T7058C", - "T7063C", - "T7109C", - "T7122C" + "T8522A" ] } - } - } - ] - }, - { - "name": "NODE_0000574", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "PP947597", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T8009C", - "A8714G" - ] + "children": [ + { + "name": "PP947644", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "PP947636", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C173T", + "G1892A", + "G8333A", + "T9803C", + "G11156A" + ], + "N": [ + "T45I" + ] + }, + "labels": { + "aa": "N: T45I" + } + } } - } + ] }, { - "name": "NODE_0000575", + "name": "NODE_0000577", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T7785C" - ] - } + "mutations": {} }, "children": [ { - "name": "NODE_0000576", + "name": "PP947645", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -63053,130 +63176,137 @@ "branch_attrs": { "mutations": { "nuc": [ - "T8522A" + "C3471T", + "G4616A", + "C8663T", + "G11945A" + ], + "F": [ + "G522E" ] - } - }, - "children": [ - { - "name": "PP947644", - "node_attrs": { - "div": 0.154, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } }, - { - "name": "PP947636", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C173T", - "G1892A", - "G8333A", - "T9803C", - "G11156A" - ], - "N": [ - "T45I" - ] - }, - "labels": { - "aa": "N: T45I" - } - } + "labels": { + "aa": "F: G522E" } - ] + } }, { - "name": "NODE_0000577", + "name": "PP947610", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "PP947645", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C3471T", - "G4616A", - "C8663T", - "G11945A" - ], - "F": [ - "G522E" - ] - }, - "labels": { - "aa": "F: G522E" - } - } - }, - { - "name": "PP947610", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G7082A", - "C9431T", - "C11327T" - ] - } - } + "mutations": { + "nuc": [ + "G7082A", + "C9431T", + "C11327T" + ] } - ] + } } ] } ] } ] - }, + } + ] + }, + { + "name": "NODE_0000578", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ { - "name": "NODE_0000578", + "name": "NODE_0000579", "node_attrs": { - "div": 0.153, + "div": 0.154, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "G3894A", + "T6626C", + "T6635C", + "T6996C", + "T6999C" + ], + "G": [ + "L127P", + "V130A", + "F162L" + ] + }, + "labels": { + "aa": "G: L127P, V130A, F162L" + } }, "children": [ { - "name": "NODE_0000579", + "name": "PP947574", "node_attrs": { - "div": 0.154, + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G1955A", + "T2093C", + "C2287T", + "C4619T", + "C4653T", + "C5217T", + "G6333A", + "G6594A", + "C6773T", + "G6968A", + "G7084A", + "G7427A", + "A8101C", + "T8144C", + "T8255A", + "G8636A", + "T10694A", + "C11810T", + "A12566G", + "C12755T" + ], + "F": [ + "A523V" + ], + "G": [ + "A166V" + ], + "L": [ + "N312T" + ] + }, + "labels": { + "aa": "F: A523V; G: A166V; L: N312T" + } + } + }, + { + "name": "PP947559", + "node_attrs": { + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -63184,27 +63314,75 @@ "branch_attrs": { "mutations": { "nuc": [ - "G3894A", - "T6626C", - "T6635C", - "T6996C", - "T6999C" + "G34A", + "T795C", + "A1400G", + "C4263T", + "C5711T", + "G5792A", + "C6387A", + "G6565A", + "T6730C", + "A7148T", + "C7283T", + "C7775T", + "G8996A", + "G9894A", + "T9945C", + "G11969A", + "G13208A" ], "G": [ - "L127P", - "V130A", - "F162L" + "A107T" + ], + "L": [ + "D910N", + "F927L" + ], + "SH": [ + "S73L", + "R100K" ] }, "labels": { - "aa": "G: L127P, V130A, F162L" + "aa": "G: A107T; L: D910N, F927L; SH: S73L, R100K" + } + } + } + ] + }, + { + "name": "NODE_0000580", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G6968A" + ] + } + }, + "children": [ + { + "name": "NODE_0000581", + "node_attrs": { + "div": 0.154, + "clade_membership": { + "value": "A2b2" } }, + "branch_attrs": { + "mutations": {} + }, "children": [ { - "name": "PP947574", + "name": "PP947622", "node_attrs": { - "div": 0.155, + "div": 0.154, "clade_membership": { "value": "A2b2" } @@ -63212,44 +63390,25 @@ "branch_attrs": { "mutations": { "nuc": [ - "G1955A", - "T2093C", - "C2287T", - "C4619T", - "C4653T", - "C5217T", - "G6333A", - "G6594A", - "C6773T", - "G6968A", - "G7084A", - "G7427A", - "A8101C", - "T8144C", - "T8255A", - "G8636A", - "T10694A", - "C11810T", - "A12566G", - "C12755T" + "T4134C", + "G4989A", + "G5297A", + "C6774T" ], - "F": [ - "A523V" - ], - "G": [ - "A166V" + "M2-1": [ + "D85N" ], - "L": [ - "N312T" + "M2-2": [ + "S17N" ] }, "labels": { - "aa": "F: A523V; G: A166V; L: N312T" + "aa": "M2-1: D85N; M2-2: S17N" } } }, { - "name": "PP947559", + "name": "NODE_0000582", "node_attrs": { "div": 0.155, "clade_membership": { @@ -63259,75 +63418,38 @@ "branch_attrs": { "mutations": { "nuc": [ - "G34A", - "T795C", - "A1400G", - "C4263T", - "C5711T", - "G5792A", - "C6387A", - "G6565A", - "T6730C", - "A7148T", - "C7283T", - "C7775T", - "G8996A", - "G9894A", - "T9945C", - "G11969A", - "G13208A" + "T4125C", + "G4667A", + "A5192G", + "T6040C", + "G6544A", + "G6785A", + "T7068C", + "C7097T", + "T7131C", + "T9896C", + "C11927T" ], - "G": [ - "A107T" + "F": [ + "S539N" ], - "L": [ - "D910N", - "F927L" + "G": [ + "E100K", + "S180N" ], "SH": [ - "S73L", - "R100K" + "S183P" ] }, "labels": { - "aa": "G: A107T; L: D910N, F927L; SH: S73L, R100K" - } - } - } - ] - }, - { - "name": "NODE_0000580", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G6968A" - ] - } - }, - "children": [ - { - "name": "NODE_0000581", - "node_attrs": { - "div": 0.153, - "clade_membership": { - "value": "A2b2" + "aa": "F: S539N; G: E100K, S180N; SH: S183P" } }, - "branch_attrs": { - "mutations": {} - }, "children": [ { - "name": "PP947622", + "name": "PP947692", "node_attrs": { - "div": 0.154, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -63335,27 +63457,43 @@ "branch_attrs": { "mutations": { "nuc": [ - "T4134C", - "G4989A", - "G5297A", - "C6774T" + "C259T", + "A1209G", + "A2097G", + "G5752A", + "G6274A", + "C6759T", + "C6774T", + "T7402C", + "A8174G", + "A8177G", + "A9893G", + "C10268T", + "A12443G", + "A12647G" ], - "M2-1": [ - "D85N" + "G": [ + "A10T" ], - "M2-2": [ - "S17N" + "L": [ + "V79A" + ], + "P": [ + "N284D" + ], + "SH": [ + "D87N" ] }, "labels": { - "aa": "M2-1: D85N; M2-2: S17N" + "aa": "G: A10T; L: V79A; P: N284D; SH: D87N" } } }, { - "name": "NODE_0000582", + "name": "PP947562", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -63363,120 +63501,82 @@ "branch_attrs": { "mutations": { "nuc": [ - "T4125C", - "G4667A", - "A5192G", - "T6040C", - "G6544A", - "G6785A", - "T7068C", - "C7097T", - "T7131C", - "T9896C", - "C11927T" - ], - "F": [ - "S539N" + "C60T", + "G638A", + "A1188G", + "G6568A", + "T8326C", + "A10256G", + "C10331T" ], "G": [ - "E100K", - "S180N" + "A108T" ], - "SH": [ - "S183P" + "L": [ + "I387T" + ], + "N": [ + "R200K" ] }, "labels": { - "aa": "F: S539N; G: E100K, S180N; SH: S183P" - } - }, - "children": [ - { - "name": "PP947692", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C259T", - "A1209G", - "A2097G", - "G5752A", - "G6274A", - "C6759T", - "C6774T", - "T7402C", - "A8174G", - "A8177G", - "A9893G", - "C10268T", - "A12443G", - "A12647G" - ], - "G": [ - "A10T" - ], - "L": [ - "V79A" - ], - "P": [ - "N284D" - ], - "SH": [ - "D87N" - ] - }, - "labels": { - "aa": "G: A10T; L: V79A; P: N284D; SH: D87N" - } - } - }, - { - "name": "PP947562", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C60T", - "G638A", - "A1188G", - "G6568A", - "T8326C", - "A10256G", - "C10331T" - ], - "G": [ - "A108T" - ], - "L": [ - "I387T" - ], - "N": [ - "R200K" - ] - }, - "labels": { - "aa": "G: A108T; L: I387T; N: R200K" - } - } + "aa": "G: A108T; L: I387T; N: R200K" } - ] + } } ] + } + ] + }, + { + "name": "NODE_0000583", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C314T", + "G5186A", + "G6028A", + "C6119A", + "G6121A", + "C6655T", + "G6890A", + "C7096T", + "T7247C", + "A7481G", + "T11048C", + "T11390C", + "C11543T", + "T11552C", + "T11648C", + "A12026G", + "C13088T" + ], + "G": [ + "P137S", + "S215N" + ], + "N": [ + "A92V" + ], + "SH": [ + "D179N" + ] }, + "labels": { + "aa": "G: P137S, S215N; N: A92V; SH: D179N" + } + }, + "children": [ { - "name": "NODE_0000583", + "name": "PP947563", "node_attrs": { - "div": 0.154, + "div": 0.155, "clade_membership": { "value": "A2b2" } @@ -63484,44 +63584,46 @@ "branch_attrs": { "mutations": { "nuc": [ - "C314T", - "G5186A", - "G6028A", - "C6119A", - "G6121A", - "C6655T", - "G6890A", - "C7096T", - "T7247C", - "A7481G", - "T11048C", - "T11390C", - "C11543T", - "T11552C", - "T11648C", - "A12026G", - "C13088T" + "C4492T", + "C5735T", + "G6790A", + "T7090C", + "T12839A" ], "G": [ - "P137S", - "S215N" - ], - "N": [ - "A92V" + "A182T" ], "SH": [ - "D179N" + "T81I" ] }, "labels": { - "aa": "G: P137S, S215N; N: A92V; SH: D179N" + "aa": "G: A182T; SH: T81I" + } + } + }, + { + "name": "NODE_0000584", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C2327T", + "A9788G", + "G10304A" + ] } }, "children": [ { - "name": "PP947563", + "name": "PP947657", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -63529,26 +63631,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C4492T", - "C5735T", - "G6790A", - "T7090C", - "T12839A" - ], - "G": [ - "A182T" - ], - "SH": [ - "T81I" + "T2600C", + "C3544T", + "G9989A" ] - }, - "labels": { - "aa": "G: A182T; SH: T81I" } } }, { - "name": "NODE_0000584", + "name": "NODE_0000585", "node_attrs": { "div": 0.155, "clade_membership": { @@ -63556,17 +63647,11 @@ } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C2327T", - "A9788G", - "G10304A" - ] - } + "mutations": {} }, "children": [ { - "name": "PP947657", + "name": "NODE_0000586", "node_attrs": { "div": 0.155, "clade_membership": { @@ -63576,15 +63661,44 @@ "branch_attrs": { "mutations": { "nuc": [ - "T2600C", - "C3544T", - "G9989A" + "A8126T" ] } - } + }, + "children": [ + { + "name": "PP947650", + "node_attrs": { + "div": 0.156, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T5985C", + "A12257G" + ] + } + } + }, + { + "name": "PP947602", + "node_attrs": { + "div": 0.155, + "clade_membership": { + "value": "A2b2" + } + }, + "branch_attrs": { + "mutations": {} + } + } + ] }, { - "name": "NODE_0000585", + "name": "NODE_0000587", "node_attrs": { "div": 0.155, "clade_membership": { @@ -63596,9 +63710,9 @@ }, "children": [ { - "name": "NODE_0000586", + "name": "PP947556", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -63606,58 +63720,42 @@ "branch_attrs": { "mutations": { "nuc": [ - "A8126T" + "A23C", + "C24-", + "G2361A", + "T6965A" + ], + "M": [ + "S66N" ] - } - }, - "children": [ - { - "name": "PP947650", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T5985C", - "A12257G" - ] - } - } }, - { - "name": "PP947602", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } + "labels": { + "aa": "M: S66N" } - ] + } }, { - "name": "NODE_0000587", + "name": "NODE_0000588", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "C4368G", + "T7994C", + "A9098G" + ] + } }, "children": [ { - "name": "PP947556", + "name": "PP947590", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -63665,24 +63763,17 @@ "branch_attrs": { "mutations": { "nuc": [ - "A23C", - "C24-", - "G2361A", - "T6965A" - ], - "M": [ - "S66N" + "G342A", + "A6357G", + "G12695A" ] - }, - "labels": { - "aa": "M: S66N" } } }, { - "name": "NODE_0000588", + "name": "NODE_0000589", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -63690,51 +63781,39 @@ "branch_attrs": { "mutations": { "nuc": [ - "C4368G", - "T7994C", - "A9098G" + "C2854T" ] } }, "children": [ { - "name": "PP947590", + "name": "PP947595", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "G342A", - "A6357G", - "G12695A" - ] - } + "mutations": {} } }, { - "name": "NODE_0000589", + "name": "NODE_0000590", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "C2854T" - ] - } + "mutations": {} }, "children": [ { - "name": "PP947595", + "name": "PP947673", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } @@ -63744,47 +63823,21 @@ } }, { - "name": "NODE_0000590", + "name": "PP947635", "node_attrs": { - "div": 0.155, + "div": 0.156, "clade_membership": { "value": "A2b2" } }, "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "PP947673", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": {} - } - }, - { - "name": "PP947635", - "node_attrs": { - "div": 0.155, - "clade_membership": { - "value": "A2b2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T3633C", - "T6965A" - ] - } - } + "mutations": { + "nuc": [ + "T3633C", + "T6965A" + ] } - ] + } } ] }