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loci.py
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loci.py
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#File that will identify any Locus as an STR or SNP
class LocusHelper:
# Values for default MiSeq analysis of CLC samples
miseqminimumSTRCoverage = None
miseqstrIT = 1.5
miseqstrAT = 4.5
miseqminimumSNPCoverage = 30
miseqsnpIT = 1.5
miseqsnpAT = 1.5
miseqhohetCutoff = 65
miseqhomomin = 90
# ----------Values for default PGM analysis of CLC samples (copied from miseq, change to match)
thermominimumSTRCoverage = None
thermostrIT = 1.5
thermostrAT = 4.5
thermominimumSNPCoverage = 100
thermosnpIT = 1.5
thermosnpAT = 4.5
thermohohetCutoff = 65
thermohomommin = 90
# Values used by ForenSeq software to identify stutter alleles (percentages)
miseqStutterFilters = {"Amelogenin":0,
"D1S1656":25,
"TPOX":10,
"D2S441":7.5,
"D2S1338":20,
"D3S1358":15,
"D4S2408":7.5,
"FGA":25,
"D5S818":12.5,
"CSF1PO":10,
"D6S1043":12.5,
"D7S820":10,
"D8S1179":25,
"D9S1122":12.5,
"D10S1248":20,
"TH01":10,
"vWA":22,
"D12S391":33,
"D13S317":12.5,
"PentaE":10,
"D16S539":20,
"D17S1301":20,
"D18S51":22,
"D19S433":12.5,
"D20S482":15,
"D21S11":10,
"PentaD":7.5,
"D22S1045":20,
"DXS10135":22,
"DXS8378":15,
"DXS7132":22,
"DXS10074":25,
"DXS10103":22,
"HPRTB":15,
"DXS7423":15,
"DYS505":15,
"DYS570":22,
"DYS576":15,
"DYS522":15,
"DYS481":50,
"DYS19":15,
"DYS391":20,
"DYS635":15,
"DYS437":45,
"DYS439":15,
"DYS389I":20,
"DYS389II":35,
"DYS438":15,
"DYS612":35,
"DYS390":15,
"DYS643":20,
"DYS533":15,
"Y-GATA-H4":35,
"DYS385a-b":20,
"DYS460":15,
"DYS549":22,
"DYS392":30,
"DYS448":15,
"DYF387S1":20}
# STR loci found in the ForenSeq Signature Prep Kit v3.0 for the Illumina MiSeq FGx
miseqSTRs = ["Amelogenin",
"D12S391",
"D17S1301",
"D18S51",
"D20S482",
"D22S1045",
"D9S1122",
"DXS10074",
"DXS10103",
"DXS10135",
"DXS7132",
"DXS7423",
"DXS8378",
"DYF387S1",
"DYS19",
"DYS385a-b",
"DYS389I",
"DYS389II",
"DYS390",
"DYS391",
"DYS392",
"DYS437",
"DYS438",
"DYS439",
"DYS448",
"DYS460",
"DYS481",
"DYS505",
"DYS522",
"DYS533",
"DYS549",
"DYS570",
"DYS576",
"DYS612",
"DYS635",
"DYS643",
"FGA",
"HPRTB",
"PentaD",
"PentaE",
"Y-GATA-H4"]
# STR loci that are found within both companies panels
bothSTRs = ["CSF1PO",
"D10S1248",
"D13S317",
"D16S539",
"D19S433",
"D1S1656",
"D21S11",
"D2S1338",
"D2S441",
"D3S1358",
"D4S2408",
"D5S818",
"D6S1043",
"D7S820",
"D8S1179",
"TH01",
"TPOX",
"vWA"]
# STRs loci that are unique to Thermo instruments
thermoSTRs = ["AMELX",
"AMELY",
"D14S1434",
"D1S1677",
"D2S1776",
"D5S2500",
"D6S474",
"D9S2157"]
# Autosomal SNPs unique to the Precision ID Identity Panel
thermoID = ["rs7520386",
"rs4847034",
"rs1872575",
"rs7704770",
"rs4288409",
"rs2016276",
"rs2292972"] #,
# "rs2534636",
# "rs35284970",
# "rs9786184",
# "rs9786139",
# "rs16981290",
# "rs17250845",
# "L298",
# "P256",
# "P202",
# "rs17306671",
# "rs4141886",
# "rs2032595",
# "rs2032599",
# "rs20320",
# "rs2032602",
# "rs8179021",
# "rs2032624",
# "rs2032636",
# "rs9341278",
# "rs2032658",
# "rs2319818",
# "rs17269816",
# "rs17222573",
# "M479",
# "rs3848982",
# "rs3900",
# "rs3911",
# "rs2032631",
# "rs2032673",
# "rs2032652",
# "rs16980426",
# "rs13447443",
# "rs17842518",
# "rs2033003"]
# Identity SNPs that are found in both Thermo and Illumina panels
bothID = ["rs1490413",
"rs560681",
"rs10495407",
"rs891700",
"rs1413212",
"rs876724",
"rs1109037",
"rs993934",
"rs12997453",
"rs907100",
"rs1357617",
"rs4364205",
"rs1355366",
"rs6444724",
"rs2046361",
"rs6811238",
"rs1979255",
"rs717302",
"rs159606",
"rs251934",
"rs338882",
"rs13218440",
"rs214955",
"rs727811",
"rs6955448",
"rs917118",
"rs321198",
"rs737681",
"rs10092491",
"rs2056277",
"rs1015250",
"rs7041158",
"rs1463729",
"rs1360288",
"rs10776839",
"rs826472",
"rs735155",
"rs3780962",
"rs740598",
"rs964681",
"rs1498553",
"rs901398",
"rs10488710",
"rs2076848",
"rs2269355",
"rs2111980",
"rs10773760",
"rs1335873",
"rs1886510",
"rs1058083",
"rs354439",
"rs1454361",
"rs722290",
"rs873196",
"rs4530059",
"rs1821380",
"rs1528460",
"rs729172",
"rs2342747",
"rs430046",
"rs1382387",
"rs9905977",
"rs740910",
"rs938283",
"rs1493232",
"rs9951171",
"rs1736442",
"rs1024116",
"rs719366",
"rs576261",
"rs1031825",
"rs445251",
"rs1005533",
"rs1523537",
"rs722098",
"rs2830795",
"rs2831700",
"rs914165",
"rs221956",
"rs733164",
"rs987640",
"rs2040411",
"rs1028528"]
# Identity SNPs that are unique to the MiSeq panel
miseqID = ["rs1294331",
"rs2399332",
"rs279844",
"rs13182883",
"rs1336071",
"rs4606077",
"rs763869",
"rs2107612",
"rs2920816",
"rs8037429",
"rs8078417"]
# SNPs unique to the Precision ID Ancestry panel for Thermo products
thermoANC = ["rs2986742",
"rs6541030",
"rs647325",
"rs4908343",
"rs1325502",
"rs12130799",
"rs3118378",
"rs1040404",
"rs1407434",
"rs4951629",
"rs316873",
"rs7421394",
"rs4666200",
"rs4670767",
"rs13400937",
"rs10496971",
"rs2627037",
"rs1569175",
"rs4955316",
"rs9809104",
"rs6548616",
"rs12629908",
"rs9845457",
"rs734873",
"rs2030763",
"rs1513181",
"rs9291090",
"rs10007810",
"rs1369093",
"rs385194",
"rs2702414",
"rs316598",
"rs37369",
"rs6451722",
"rs12657828",
"rs6556352",
"rs1500127",
"rs6422347",
"rs1040045",
"rs2504853",
"rs7745461",
"rs4463276",
"rs4458655",
"rs1871428",
"rs731257",
"rs32314",
"rs2330442",
"rs4717865",
"rs10954737",
"rs705308",
"rs7803075",
"rs10236187",
"rs6464211",
"rs10108270",
"rs3943253",
"rs1471939",
"rs12544346",
"rs7844723",
"rs2001907",
"rs10511828",
"rs3793451",
"rs2306040",
"rs10513300",
"rs2073821",
"rs3793791",
"rs4746136",
"rs4918842",
"rs4880436",
"rs10839880",
"rs1837606",
"rs2946788",
"rs11227699",
"rs948028",
"rs2416791",
"rs1513056",
"rs214678",
"rs772262",
"rs2070586",
"rs1503767",
"rs9319336",
"rs9530435",
"rs1760921",
"rs2357442",
"rs1950993",
"rs8021730",
"rs946918",
"rs3784230",
"rs2899826",
"rs8035124",
"rs4984913",
"rs4781011",
"rs818386",
"rs2966849",
"rs1879488",
"rs2033111",
"rs10512572",
"rs2125345",
"rs4798812",
"rs7238445",
"rs881728",
"rs874299",
"rs8113143",
"rs3745099",
"rs2532060",
"rs6104567",
"rs3907047",
"rs2835370",
"rs1296819",
"rs4821004",
"rs5768007"]
# Ancestry SNPs that are found in both company's panels
bothANC = ["rs3737576",
"rs7554936",
"rs2814778",
"rs798443",
"rs1876482",
"rs1834619",
"rs3827760",
"rs260690",
"rs6754311",
"rs10497191",
"rs12498138",
"rs4833103",
"rs1229984",
"rs3811801",
"rs7657799",
"rs870347",
"rs16891982",
"rs7722456",
"rs192655",
"rs3823159",
"rs917115",
"rs1462906",
"rs6990312",
"rs2196051",
"rs1871534",
"rs3814134",
"rs4918664",
"rs174570",
"rs1079597",
"rs2238151",
"rs671",
"rs7997709",
"rs1572018",
"rs2166624",
"rs7326934",
"rs9522149",
"rs200354",
"rs1800414",
"rs12913832",
"rs12439433",
"rs735480",
"rs1426654",
"rs459920",
"rs4411548",
"rs2593595",
"rs17642714",
"rs4471745",
"rs11652805",
"rs2042762",
"rs7226659",
"rs3916235",
"rs4891825",
"rs7251928",
"rs310644",
"rs2024566"]
# The single unique Ancestry SNP for MiSeq
miseqANC = ["rs1919550"]
#The SNPs used by the Forenseq software for phenotypic purposes
miseqPHENO = ["rs28777",
"rs12203592",
"rs4959270",
"rs683",
"rs1042602",
"rs1393350",
"rs12821256",
"rs12896399",
"rs2402130",
"rs1800407",
"rs312262906_N29insA",
"N29insA",
"rs1110400",
"rs11547464",
"rs1805005",
"rs1805006",
"rs1805007",
"rs1805008",
"rs1805009",
"rs201326893_Y152OCH",
"rs2228479",
"rs885479",
"rs2378249"]
# SNPs found in the Precision ID kit that are used to identify the sex of the sample
ySNPs = ["rs2534636",
"rs35284970",
"rs9786184",
"rs9786139",
"rs16981290",
"rs17250845",
"L298",
"rs372687543",
"P256",
"P202",
"rs369616152",
"rs17306671",
"rs4141886",
"rs2032595",
"rs2032599",
"rs20320",
"rs2032602",
"rs8179021",
"rs2032624",
"rs2032636",
"rs9341278",
"rs2032658",
"rs2319818",
"rs17269816",
"rs17222573",
"M479",
"rs372157627",
"rs3848982",
"rs3900",
"rs3911",
"rs2032631",
"rs2032673",
"rs2032652",
"rs16980426",
"rs13447443",
"rs17842518",
"rs2033003"]
locusPositions = {"AmelogeninY":["Y","TBD"],
"AmelogeninX":["X","TBD"],
"Amelogenin":["X/Y","TBD"],
"AMELY":["Y","TBD"],
"AMELX":["X","TBD"],
"D12S391":["12","TBD"],
"D17S1301":["17","TBD"],
"D18S51":["18","TBD"],
"D20S482":["20","TBD"],
"D22S1045":["22","TBD"],
"D9S1122":["9","TBD"],
"DXS10074":["X","TBD"],
"DXS10103":["X","TBD"],
"DXS10135":["X","TBD"],
"DXS7132":["X","TBD"],
"DXS7423":["X","TBD"],
"DXS8378":["X","TBD"],
"DYF387S1":["Y","TBD"],
"DYS19":["Y","TBD"],
"DYS385a-b":["Y","TBD"],
"DYS389I":["Y","TBD"],
"DYS389II":["Y","TBD"],
"DYS390":["Y","TBD"],
"DYS391":["Y","TBD"],
"DYS392":["Y","TBD"],
"DYS437":["Y","TBD"],
"DYS438":["Y","TBD"],
"DYS439":["Y","TBD"],
"DYS448":["Y","TBD"],
"DYS460":["Y","TBD"],
"DYS481":["Y","TBD"],
"DYS505":["Y","TBD"],
"DYS522":["Y","TBD"],
"DYS533":["Y","TBD"],
"DYS549":["Y","TBD"],
"DYS570":["Y","TBD"],
"DYS576":["Y","TBD"],
"DYS612":["Y","TBD"],
"DYS635":["Y","TBD"],
"DYS643":["Y","TBD"],
"FGA":["4","TBD"],
"HPRTB":["X","TBD"],
"PentaD":["21","TBD"],
"PentaE":["15","TBD"],
"Y-GATA-H4":["Y","TBD"],
"CSF1PO":["5","TBD"],
"D10S1248":["10","TBD"],
"D13S317":["13","TBD"],
"D16S539":["16","TBD"],
"D19S433":["19","TBD"],
"D1S1656":["1","TBD"],
"D21S11":["21","TBD"],
"D2S1338":["2","TBD"],
"D2S441":["2","TBD"],
"D3S1358":["3","TBD"],
"D4S2408":["4","TBD"],
"D5S818":["5","TBD"],
"D6S1043":["6","TBD"],
"D7S820":["7","TBD"],
"D8S1179":["8","TBD"],
"TH01":["11","TBD"],
"TPOX":["2","TBD"],
"vWA":["12","TBD"],
"D14S1434":["14","TBD"],
"D1S1677":["1","TBD"],
"D2S1776":["2","TBD"],
"D5S2500":["5","TBD"],
"D6S474":["6","TBD"],
"D9S2157":["9","TBD"],
"rs7520386":["1","14155402"],
"rs4847034":["1","105717631"],
"rs1872575":["3","113804979"],
"rs7704770":["5","159487953"],
"rs4288409":["8","136839229"],
"rs2016276":["15","24571796"],
"rs2292972":["17","80765788"],
"rs2534636":["Y","2657176"],
"rs35284970":["Y","2734854"],
"rs9786184":["Y","2887824"],
"rs9786139":["Y","6753519"],
"rs16981290":["Y","7568568"],
"rs17250845":["Y","8418927"],
"L298":["Y","8467290"],
"P256":["Y","8685230"],
"P202":["Y","14001024"],
"rs17306671":["Y","14031334"],
"rs4141886":["Y","14197867"],
"rs2032595":["Y","14813991"],
"rs2032599":["Y","14851554"],
"rs20320":["Y","14898163"],
"rs2032602":["Y","14954280"],
"rs8179021":["Y","15018582"],
"rs2032624":["Y","15026424"],
"rs2032636":["Y","15027529"],
"rs9341278":["Y","15469724"],
"rs2032658":["Y","15581983"],
"rs2319818":["Y","16354708"],
"rs17269816":["Y","17053771"],
"rs17222573":["Y","17891241"],
"M479":["Y","20834667"],
"rs3848982":["Y","21717208"],
"rs3900":["Y","21730257"],
"rs3911":["Y","21733454"],
"rs2032631":["Y","21867787"],
"rs2032673":["Y","21894058"],
"rs2032652":["Y","21917313"],
"rs16980426":["Y","22214221"],
"rs13447443":["Y","22739301"],
"rs17842518":["Y","23443971"],
"rs2033003":["Y","23550924"],
"rs1490413":["1","4367323"],
"rs560681":["1","160786670"],
"rs10495407":["1","238439308"],
"rs891700":["1","239881926"],
"rs1413212":["1","242806797"],
"rs876724":["2","114974"],
"rs1109037":["2","10085722"],
"rs993934":["2","124109213"],
"rs12997453":["2","182413259"],
"rs907100":["2","239563579"],
"rs1357617":["3","961782"],
"rs4364205":["3","32417644"],
"rs1355366":["3","190806108"],
"rs6444724":["3","193207380"],
"rs2046361":["4","10969059"],
"rs6811238":["4","169663615"],
"rs1979255":["4","190318080"],
"rs717302":["5","2879395"],
"rs159606":["5","17374898"],
"rs251934":["5","174778678"],
"rs338882":["5","178690725"],
"rs13218440":["6","12059954"],
"rs214955":["6","152697706"],
"rs727811":["6","165045334"],
"rs6955448":["7","4310365"],
"rs917118":["7","4457003"],
"rs321198":["7","137029838"],
"rs737681":["7","155990813"],
"rs10092491":["8","28411072"],
"rs2056277":["8","139399116"],
"rs1015250":["9","1823774"],
"rs7041158":["9","27985938"],
"rs1463729":["9","126881448"],
"rs1360288":["9","128968063"],
"rs10776839":["9","137417308"],
"rs826472":["10","2406631"],
"rs735155":["10","3374178"],
"rs3780962":["10","17193346"],
"rs740598":["10","118506899"],
"rs964681":["10","132698419"],
"rs1498553":["11","5709028"],
"rs901398":["11","11096221"],
"rs10488710":["11","115207176"],
"rs2076848":["11","134667546"],
"rs2269355":["12","6945914"],
"rs2111980":["12","106328254"],
"rs10773760":["12","130761696"],
"rs1335873":["13","20901724"],
"rs1886510":["13","22374700"],
"rs1058083":["13","100038233"],
"rs354439":["13","106938411"],
"rs1454361":["14","25850832"],
"rs722290":["14","53216723"],
"rs873196":["14","98845531"],
"rs4530059":["14","104769149"],
"rs1821380":["15","39313402"],
"rs1528460":["15","55210705"],
"rs729172":["16","5606197"],
"rs2342747":["16","5868700"],
"rs430046":["16","78017051"],
"rs1382387":["16","80106361"],
"rs9905977":["17","2919393"],
"rs740910":["17","5706623"],
"rs938283":["17","77468498"],
"rs1493232":["18","1127986"],
"rs9951171":["18","9749879"],
"rs1736442":["18","55225777"],
"rs1024116":["18","75432386"],
"rs719366":["19","28463337"],
"rs576261":["19","39559807"],
"rs1031825":["20","4447483"],
"rs445251":["20","15124933"],
"rs1005533":["20","39487110"],
"rs1523537":["20","51296162"],
"rs722098":["21","16685598"],
"rs2830795":["21","28608163"],
"rs2831700":["21","29679687"],
"rs914165":["21","42415929"],
"rs221956":["21","43606997"],
"rs733164":["22","27816784"],
"rs987640":["22","33559508"],
"rs2040411":["22","47836412"],
"rs1028528":["22","48362290"],
"rs1294331":["1","233448413"],
"rs2399332":["3","110301126"],
"rs279844":["4","46329655"],
"rs13182883":["5","136633338"],
"rs1336071":["6","94537255"],
"rs4606077":["8","144656754"],
"rs763869":["8","1375610"],
"rs2107612":["12","888320"],
"rs2920816":["12","40863052"],
"rs8037429":["15","53616909"],
"rs8078417":["17","80461935"],
"rs2986742":["1","6550376"],
"rs6541030":["1","12608178"],
"rs647325":["1","18170886"],
"rs4908343":["1","27931698"],
"rs1325502":["1","42360270"],
"rs12130799":["1","55663372"],
"rs3118378":["1","68849687"],
"rs1040404":["1","168159890"],
"rs1407434":["1","186149032"],
"rs4951629":["1","212786883"],
"rs316873":["1","242342504"],
"rs7421394":["2","14756349"],
"rs4666200":["2","29538411"],
"rs4670767":["2","37941396"],
"rs13400937":["2","79864923"],
"rs10496971":["2","145769943"],
"rs2627037":["2","179606538"],
"rs1569175":["2","201021954"],
"rs4955316":["3","30415612"],
"rs9809104":["3","39146429"],
"rs6548616":["3","79399575"],
"rs12629908":["3","120522716"],
"rs9845457":["3","135914476"],
"rs734873":["3","147750355"],
"rs2030763":["3","179964727"],
"rs1513181":["3","188574996"],
"rs9291090":["4","5390637"],
"rs10007810":["4","41554364"],
"rs1369093":["4","73245191"],
"rs385194":["4","85309078"],
"rs2702414":["4","179399523"],
"rs316598":["5","2364626"],
"rs37369":["5","35037115"],
"rs6451722":["5","43711378"],
"rs12657828":["5","79085726"],
"rs6556352":["5","155471714"],
"rs1500127":["5","165739982"],
"rs6422347":["5","177863083"],
"rs1040045":["6","4747159"],
"rs2504853":["6","12535111"],
"rs7745461":["6","21911616"],
"rs4463276":["6","145055331"],
"rs4458655":["6","163221792"],
"rs1871428":["6","168665760"],
"rs731257":["7","12669251"],
"rs32314":["7","32179124"],
"rs2330442":["7","42380071"],
"rs4717865":["7","73454199"],
"rs10954737":["7","83533047"],
"rs705308":["7","97695363"],
"rs7803075":["7","130742066"],
"rs10236187":["7","139447377"],
"rs6464211":["7","151873853"],
"rs10108270":["8","4190793"],
"rs3943253":["8","13359500"],
"rs1471939":["8","28941305"],
"rs12544346":["8","86424616"],
"rs7844723":["8","122908503"],
"rs2001907":["8","140241181"],
"rs10511828":["9","28628500"],
"rs3793451":["9","71659280"],
"rs2306040":["9","93641199"],
"rs10513300":["9","120130206"],
"rs2073821":["9","135933122"],
"rs3793791":["10","50841704"],
"rs4746136":["10","75300994"],
"rs4918842":["10","115316812"],
"rs4880436":["10","134650103"],
"rs10839880":["11","7850316"],
"rs1837606":["11","15838137"],
"rs2946788":["11","24010530"],
"rs11227699":["11","66898492"],
"rs948028":["11","120644447"],
"rs2416791":["12","11701488"],
"rs1513056":["12","17407792"],
"rs214678":["12","47676950"],
"rs772262":["12","56163734"],
"rs2070586":["12","109277720"],
"rs1503767":["12","118889488"],
"rs9319336":["13","27624356"],
"rs9530435":["13","75993887"],
"rs1760921":["14","20818131"],
"rs2357442":["14","52607967"],
"rs1950993":["14","58238687"],
"rs8021730":["14","67886781"],
"rs946918":["14","83472868"],
"rs3784230":["14","105679055"],
"rs2899826":["15","74734500"],
"rs8035124":["15","92105708"],
"rs4984913":["16","740466"],
"rs4781011":["16","10975311"],
"rs818386":["16","65406708"],
"rs2966849":["16","85183682"],
"rs1879488":["17","1401613"],
"rs2033111":["17","53788280"],
"rs10512572":["17","69512099"],
"rs2125345":["17","73782191"],
"rs4798812":["18","9420504"],
"rs7238445":["18","49781544"],
"rs881728":["18","59333108"],
"rs874299":["18","75056284"],
"rs8113143":["19","33652247"],
"rs3745099":["19","52901905"],
"rs2532060":["19","55614923"],
"rs6104567":["20","10195433"],
"rs3907047":["20","54000914"],
"rs2835370":["21","37885625"],
"rs1296819":["22","18076546"],
"rs4821004":["22","32366359"],
"rs5768007":["22","48207872"],
"rs3737576":["1","101709563"],
"rs7554936":["1","151122489"],
"rs2814778":["1","159174683"],
"rs798443":["2","7968275"],
"rs1876482":["2","17362568"],
"rs1834619":["2","17901485"],
"rs3827760":["2","109513601"],
"rs260690":["2","109579738"],
"rs6754311":["2","136707982"],
"rs10497191":["2","158667217"],
"rs12498138":["3","121459589"],
"rs4833103":["4","38815502"],
"rs1229984":["4","100239319"],
"rs3811801":["4","100244319"],
"rs7657799":["4","105375423"],
"rs870347":["5","6845035"],
"rs16891982":["5","33951693"],
"rs7722456":["5","170202984"],
"rs192655":["6","90518278"],
"rs3823159":["6","136482727"],
"rs917115":["7","28172586"],
"rs1462906":["8","31896592"],
"rs6990312":["8","110602317"],
"rs2196051":["8","122124302"],
"rs1871534":["8","145639681"],
"rs3814134":["9","127267689"],
"rs4918664":["10","94921065"],
"rs174570":["11","61597212"],
"rs1079597":["11","113296286"],
"rs2238151":["12","112211833"],
"rs671":["12","112241766"],
"rs7997709":["13","34847737"],
"rs1572018":["13","41715282"],
"rs2166624":["13","42579985"],
"rs7326934":["13","49070512"],
"rs9522149":["13","111827167"],
"rs200354":["14","99375321"],
"rs1800414":["15","28197037"],
"rs12913832":["15","28365618"],
"rs12439433":["15","36220035"],
"rs735480":["15","45152371"],
"rs1426654":["15","48426484"],
"rs459920":["16","89730827"],
"rs4411548":["17","40658533"],
"rs2593595":["17","41056245"],
"rs17642714":["17","48726132"],
"rs4471745":["17","53568884"],
"rs11652805":["17","62987151"],
"rs2042762":["18","35277622"],
"rs7226659":["18","40488279"],
"rs3916235":["18","67578931"],
"rs4891825":["18","67867663"],
"rs7251928":["19","4077096"],
"rs310644":["20","62159504"],
"rs2024566":["22","41697338"],
"rs1919550":["3","121364173"],
"rs28777":["5","33958959"],
"rs12203592":["6","396321"],
"rs4959270":["6","457748"],
"rs683":["9","12709305"],
"rs1042602":["11","88911696"],
"rs1393350":["11","89011046"],
"rs12821256":["12","89328335"],
"rs12896399":["14","92773663"],
"rs2402130":["14","92801203"],
"rs1800407":["15","28230318"],
"rs312262906_N29insA":["16","89985753"],
"N29insA":["16","89985753"],
"rs1110400":["16","89986130"],
"rs11547464":["16","89986091"],
"rs1805005":["16","89985844"],
"rs1805006":["16","89985918"],
"rs1805007":["16","89986117"],
"rs1805008":["16","89986144"],
"rs1805009":["16","89986546"],
"rs201326893_Y152OCH":["16","89986122"],
"rs2228479":["16","89985940"],
"rs885479":["16","89986154"],
"rs2378249":["20","33218090"],
"rs369616152":["Y", "TBD"],
"rs372157627":["Y", "TBD"],
"rs372687543":["Y", "TBD"]}
# A conglomerate of all SNPs
allSNPs = thermoID + miseqID + bothID + thermoANC + miseqANC + bothANC + miseqPHENO + ySNPs
# A conglomerate of all STRs
allSTRs = thermoSTRs + miseqSTRs + bothSTRs