diff --git a/nextclade/config/config_dengue.yaml b/nextclade/config/config_dengue.yaml index f67acae0..ed088a2e 100644 --- a/nextclade/config/config_dengue.yaml +++ b/nextclade/config/config_dengue.yaml @@ -21,6 +21,14 @@ filter: denv3: '36' denv4: '36' +refine: + root_id: + all: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome" + denv1: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome" + denv2: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome" + denv3: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome" + denv4: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome" + traits: sampling_bias_correction: '3' traits_columns: diff --git a/nextclade/datasets/all/README.md b/nextclade/datasets/all/README.md index cc205180..affdf57a 100644 --- a/nextclade/datasets/all/README.md +++ b/nextclade/datasets/all/README.md @@ -1,7 +1,26 @@ -# Nextclade dataset for "Dengue Virus" +# De dataset -## Dataset attributes +| Key | Value | +| :-- | :-- | +| name | Dengue (serotype-level) | +| authors | [Nextstrain](https://nextstrain.org) | +| reference | NC_002640.1 | +| workflow | https://github.com/nextstrain/dengue/tree/main/nextclade | +| path | `nextstrain/dengue/all` | -Nextclade dataset -Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html +## Scope of this dataset + +This dataset assigns serotype to dengue samples based on [criteria outlined by the WHO](https://pubmed.ncbi.nlm.nih.gov/26868382/) and tree placement nearest references [NC_001477.1 (DENV1)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001477.1), [NC_001474.2 (DENV2)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001474.2), [NC_001475.2 (DENV3)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001475.2), and [NC_002640.1 (DENV4)](https://www.ncbi.nlm.nih.gov/nuccore/NC_002640.1). + +## Features + +This dataset supports: + +- Assignment of serotypes +- Phylogenetic placement +- Sequence quality control (QC) + +## What are Nextclade datasets + +Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/nextclade/datasets/all/genome_annotation.gff3 b/nextclade/datasets/all/genome_annotation.gff3 index a417d706..3d63959e 100644 --- a/nextclade/datasets/all/genome_annotation.gff3 +++ b/nextclade/datasets/all/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_002640.1 1 10649 -NC_002640.1 feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; -NC_002640.1 feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; -NC_002640.1 feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; -NC_002640.1 feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; -NC_002640.1 feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_002640.1 feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_002640.1 feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_002640.1 feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_002640.1 feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_002640.1 feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; -NC_002640.1 feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_002640.1 feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome 1 10649 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/datasets/all/pathogen.json b/nextclade/datasets/all/pathogen.json index b7ecb9fe..356c11db 100644 --- a/nextclade/datasets/all/pathogen.json +++ b/nextclade/datasets/all/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.01, "minLength": 1000 }, @@ -30,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -56,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/datasets/all/reference.fasta b/nextclade/datasets/all/reference.fasta index 1abd4ccc..08495c13 100644 --- a/nextclade/datasets/all/reference.fasta +++ b/nextclade/datasets/all/reference.fasta @@ -1,179 +1,2 @@ ->NC_002640.1 Dengue virus 4, complete genome -AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAG -TTCTAACAGTTTGTTTGAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGG -TGGTTAGACCACCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAG -GGTTGGTGAAGAGATTCTCAACCGGACTTTTTTCTGGGAAAGGACCCTTACGGATGGTGC -TAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAGA -GATGGGGACAGTTGAAGAAAAATAAGGCCATCAAGATACTGATTGGATTCAGGAAGGAGA -TAGGCCGCATGCTGAACATCTTGAACGGGAGAAAAAGGTCAACGATAACATTGCTGTGCT -TGATTCCCACCGTAATGGCGTTTTCCCTCAGCACAAGAGATGGCGAACCCCTCATGATAG -TGGCAAAACATGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAAT -GCACTCTCATTGCCATGGACTTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCC -CCCTACTGGTCAATACCGAACCTGAAGACATTGATTGCTGGTGCAACCTCACGTCTACCT -GGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAG -CTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGGATGTCATCGG -AAGGGGCTTGGAAGCATGCTCAGAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCG -CGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCT -TCTTTGTCCTAATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAA -ACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATG -GAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGA -CAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACA -TAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACC -AACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGT -TTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCA -ATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACA -CCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGT -CACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCA -GGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCG -TGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAG -AGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGAC -AGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCA -CAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTTAAGTGCAAAGTCC -GTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAA -TTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAG -GTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGG -TTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAG -AATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAA -CACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAG -GTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGAC -TGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGT -TTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCA -CGAACTCGAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGT -TTCTGGGCTTCACAGTTCAAGCAGACATGGGTTGTGTGGCGTCATGGAGTGGGAAAGAAT -TGAAGTGTGGAAGCGGAATTTTTGTGGTTGACAACGTGCACACTTGGACAGAACAGTACA -AATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCTGCAATATTAAATGCCCACAAAGATG -GGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAGCAAATAACCA -ACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTAGTGGCTGGGGATG -TGAAGGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCCCCAGTGAGTGATCTGAAAT -ATTCATGGAAGACATGGGGAAAAGCAAAAATCTTCACCCCAGAAGCAAGAAATAGCACAT -TTTTAATAGACGGACCAGACACCTCTGAATGCCCCAATGAACGAAGAGCATGGAACTCTC -TTGAGGTGGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTCCGAG -AAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCTGCAATTAAAGATCAGAAAG -CTGTGCATGCTGACATGGGTTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAG -AGAAAGCATCTCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACCCACACACTGTGGA -GCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAATCATATGCGGGCCCTTTTTCAC -AGCACAATTACCGCCAGGGCTATGCCACGCAAACCGTGGGCCCATGGCACTTAGGCAAAT -TAGAGATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACC -ATAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAACTAGTCACGCAATGGTGCT -GCCGCTCCTGCACGATGCCTCCCTTAAGGTTCTTGGGAGAAGATGGGTGCTGGTATGGGA -TGGAGATTAGGCCCTTGAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGACGGCCG -GACAGGGCACATCAGAAACTTTTTCTATGGGTCTGTTGTGCCTGACCTTGTTTGTGGAAG -AATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTAGTTGTGGTGATCACTCTTT -GTGCTATCATCCTGGGAGGCCTCACATGGATGGACTTACTACGAGCCCTCATCATGTTGG -GGGACACTATGTCTGGTAGAATAGGAGGACAGATCCACCTAGCCATCATGGCAGTGTTCA -AGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAG -CACTAATGGTAATAGGAATGGCCATGACAACGGTGCTTTCAATTCCACATGACCTTATGG -AACTCATTGATGGAATATCACTGGGACTAATTTTGCTAAAAATAGTAACACAGTTTGACA -ACACCCAAGTGGGAACCTTAGCTCTTTCCTTGACTTTCATAAGATCAACAATGCCATTGG -TCATGGCTTGGAGGACCATTATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTGTGCA -GGACAAGCTGTCTTCAAAAACAGTCTCATTGGGTAGAAATAACAGCACTCATCCTAGGAG -CCCAAGCTCTGCCAGTGTACCTAATGACTCTTATGAAAGGAGCCTCAAGAAGATCTTGGC -CTCTTAACGAGGGCATAATGGCTGTGGGTTTGGTTAGTCTCTTAGGAAGCGCTCTTTTAA -AGAATGATGTCCCTTTAGCTGGCCCAATGGTGGCAGGAGGCTTACTTCTGGCGGCTTACG -TGATGAGTGGTAGCTCAGCAGATCTGTCACTAGAGAAGGCCGCCAACGTGCAGTGGGATG -AAATGGCAGACATAACAGGCTCAAGCCCAATCGTAGAAGTGAAGCAGGATGAAGATGGCT -CTTTCTCCATACGGGACGTCGAGGAAACCAATATGATAACCCTTTTGGTGAAACTGGCAC -TGATAACAGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACCTTATGGTACA -TGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTCCCCTCACCCGCTGCCA -CTAAAAAAGCCGCACTGTCTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTATTCGGGA -AAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAA -CAAGAGGATCAGTGATCTGCCACGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCA -GGAATGACATGATATCATACGGTGGGGGATGGAGGCTTGGAGACAAATGGGACAAAGAAG -AAGACGTTCAGGTCCTCGCCATAGAACCAGGAAAAAATCCTAAACATGTCCAAACGAAAC -CTGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTAGATTTCAAACCCG -GAACGTCTGGTTCTCCCATCATCAACAGGAAAGGAAAAGTCATCGGACTCTATGGAAATG -GAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGAG -AGCCAGATTATGAAGTGGATGAGGACATTTTTCGAAAGAAAAGATTAACTATAATGGACT -TACACCCCGGAGCTGGAAAGACAAAAAGAATTCTTCCATCAATAGTGAGAGAAGCCTTAA -AAAGGAGGCTACGAACTTTGATTTTAGCTCCCACGAGAGTGGTGGCGGCCGAGATGGAAG -AGGCCCTACGTGGACTGCCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAG -GAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTTTTGTCATCAA -CCAGGGTTCCAAATTACAACCTTATAGTGATGGATGAAGCACATTTCACCGATCCTTCTA -GTGTCGCGGCTAGAGGATACATCTCGACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCT -TCATGACCGCAACCCCTCCCGGAGCGACAGATCCCTTTCCCCAGAGCAACAGCCCAATAG -AAGACATCGAGAGGGAAATTCCGGAAAGGTCATGGAACACAGGGTTCGACTGGATAACAG -ACTACCAAGGGAAAACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAA -ATTGTTTGAGAAAGTCGGGAAAGAAAGTTATCCAGTTGAGTAGGAAAACCTTTGATACAG -AGTATCCAAAAACGAAACTCACGGACTGGGACTTTGTGGTCACTACAGACATATCTGAAA -TGGGGGCCAATTTTAGAGCCGGGAGAGTGATAGACCCTAGAAGATGCCTCAAGCCAGTTA -TCCTACCAGATGGGCCAGAGAGAGTCATTTTAGCAGGTCCTATTCCAGTGACTCCAGCAA -GCGCTGCTCAGAGAAGAGGGCGAATAGGAAGGAACCCAGCACAAGAAGACGACCAATACG -TTTTCTCCGGAGACCCACTAAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGA -TGCTGCTTGACAATATCTACACCCCAGAAGGGATCATTCCAACATTGTTTGGTCCGGAAA -GGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTT -TTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCTG -CTGGCATTTCTTACGAAGATCGGGAATGGTGCTTCACAGGGGAAAGAAATAACCAAATTT -TAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAGCTAAGGC -CAAGATGGTTAGATGCACGTGTATACGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGT -TTGCCAGTGGAAGGAAGAGTATAACTCTCGACATCCTAACAGAGATTGCCAGTTTGCCAA -CTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGATAACATAGTCATGCTCCACACAACAG -AAAGAGGAGGGAGGGCCTATCAACACGCCCTGAACGAACTTCCGGAGTCACTGGAAACAC -TCATGCTTGTAGCTTTACTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTCATGCAAG -GGAAAGGAATAGGGAAATTGTCAATGGGTTTGATAACCATTGCGGTGGCTAGTGGCTTGC -TCTGGGTAGCAGAAATTCAACCCCAGTGGATAGCGGCCTCAATCATACTAGAGTTTTTTC -TCATGGTACTGTTGATACCGGAACCAGAAAAACAAAGGACCCCACAAGACAATCAATTGA -TCTACGTCATATTGACCATTCTCACCATCATTGGTCTAATAGCAGCCAACGAGATGGGGC -TGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCC -TCGATGTGGACTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACAATTC -TGACTCCCATGCTGAGACACACCATAGAAAACACGTCGGCCAACCTATCTCTAGCAGCCA -TTGCCAACCAGGCAGCCGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGG -ACCTCGGTGTGCCGCTGTTAGCAATGGGATGCTATTCTCAAGTGAACCCAACAACCTTGA -CAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGCCCAGGATTGCAGGCAA -AAGCCACAAGAGAGGCCCAGAAAAGGACAGCTGCTGGGATCATGAAAAATCCCACAGTGG -ACGGGATAACAGTAATAGATCTAGAACCAATATCCTATGACCCAAAATTTGAAAAGCAAT -TAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACAT -GGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAATCTTGACCTTGTGGGAGGGCA -ACCCGGGAAGGTTTTGGAACACGACCATAGCCGTATCCACCGCCAACATTTTCAGGGGAA -GTTACTTGGCGGGAGCTGGACTGGCTTTTTCACTCATAAAGAATGCACAAACCCCTAGGA -GGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCAT -TAGACAGAAAAGAGTTTGAAGAGTATAAAAGAAGTGGAATACTAGAAGTGGACAGGACTG -AAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTATCAAGAGGGTCCA -GTAAGATCAGATGGATTGTTGAGAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTAGATC -TTGGCTGTGGGAGAGGAGGATGGTCTTATTACATGGCGACACTCAAGAACGTGACTGAAG -TGAAAGGGTATACAAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACTTATG -GTTGGAATTTGGTCAAACTCCATTCAGGGGTTGACGTGTTCTACAAACCCACAGAGCAAG -TGGACACCCTGCTCTGTGATATTGGGGAGTCATCTTCTAATCCAACAATAGAGGAAGGAA -GAACATTAAGAGTTTTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCA -TCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAGCTGGAGAAACTGCAGAGAA -AACATGGTGGGAACCTTGTCAGATGCCCGCTGTCCAGGAACTCCACCCATGAGATGTATT -GGGTGTCAGGAGCGTCGGGAAACATTGTGAGCTCTGTGAACACAACATCAAAGATGTTGT -TGAACAGGTTCACAACAAGGCATAGGAAACCCACTTATGAGAAGGACGTAGATCTTGGGG -CAGGAACGAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAA -GGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACCTGGCATTATGATCAGGAAAACCCAT -ACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCTGCATCCTCCA -TGGTGAACGGGGTGGTAAAACTGCTAACAAAACCCTGGGATGTGATTCCAATGGTGACTC -AGTTAGCCATGACAGATACAACCCCTTTTGGGCAACAAAGAGTGTTCAAAGAGAAGGTGG -ATACCAGAACACCACAACCAAAACCCGGTACACGAATGGTTATGACCACGACAGCCAATT -GGCTGTGGGCCCTCCTTGGAAAGAAGAAAAATCCCAGACTGTGCACAAGGGAAGAGTTCA -TCTCAAAAGTTAGATCAAACGCAGCCATAGGCGCAGTCTTTCAGGAAGAACAGGGATGGA -CATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGG -CCCTACACCAGGAAGGGAAATGTGAATCGTGTGTCTATAACATGATGGGAAAACGTGAGA -AAAAGTTAGGAGAGTTTGGCAGAGCCAAGGGAAGCCGAGCAATCTGGTACATGTGGCTGG -GAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTTTTGAATGAAGATCACTGGTTTGGCA -GAGAAAATTCATGGAGTGGAGTGGAAGGGGAAGGTCTGCACAGATTGGGATATATCCTGG -AGGAGATAGACAAGAAGGATGGAGACCTAATGTATGCTGATGACACAGCAGGCTGGGACA -CAAGAATCACTGAGGATGACCTTCAAAATGAGGAACTGATCACGGAACAGATGGCTCCCC -ACCACAAGATCCTAGCCAAAGCCATTTTCAAACTAACCTATCAAAACAAAGTGGTGAAAG -TCCTCAGACCCACACCGCGGGGAGCGGTGATGGATATCATATCCAGGAAAGACCAAAGAG -GTAGTGGACAAGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTTCAACTCA -TCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGT -TGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTAAAGAGGATGG -CAATCAGTGGAGACGATTGCGTGGTGAAGCCCCTAGATGAGAGGTTTGGCACTTCCCTCC -TCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCTAAGG -GATGGAAAAACTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTTATGA -AGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCA -GAATCTCGCAGGGAGCTGGATGGAGCTTAAGAGAAACAGCCTGCCTGGGCAAAGCTTACG -CCCAGATGTGGTCGCTTATGTACTTCCACAGAAGGGATCTGCGTTTAGCCTCCATGGCCA -TATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACG -CTCATCACCAGTGGATGACCACTGAAGATATGCTCAAAGTGTGGAACAGAGTGTGGATAG -AAGACAACCCTAATATGACTGACAAGACTCCAGTCCATTCGTGGGAAGATATACCTTACC -TAGGGAAAAGAGAGGATTTGTGGTGTGGATCCCTGATTGGACTTTCTTCCAGAGCCACCT -GGGCGAAGAACATTCATACGGCCATAACCCAGGTCAGGAACCTGATCGGAAAAGAGGAAT -ACGTGGATTACATGCCAGTAATGAAAAGATACAGTGCTCCTTCAGAGAGTGAAGGAGTTC -TGTAATTACCAACAACAAACACCAAAGGCTATTGAAGTCAGGCCACTTGTGCCACGGTTT -GAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAATGGGAGGCGTAATAATCCCCAGGGAG -GCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCT -CCCATCACTGATAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTG -GTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGG -GAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGAT -GGATTGGTGTTGTTGATCCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome 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TCTGGAACAGGGTGTGGATAGAGGACAACCCATGGATGGAAGACAAAACTCCAGTCTAATCTTGGGAAGACATACCATACCTAGGGAAAAGAGAAGACCAGTGGTGTGGATCCCTGATTGGCCTAACATCCAGGGCCACCTGGGCAAAGAACATTCAAACAGCCATAAACCAAGTCAGAAGCCTCATTGGGAATGAGGAGTATATAGATTACATGCCATCAATGAAAAGATTCAGGAATGAGGAGGAGAACGAAGGAGTTCTGTGGTAAACAGCAAAAGAAGTCAGGCATAAAAGAAGTCAGGCCACTAATGCCACGGCTTGAGCAAACCGTGCTGCCTGTAGCTCCACCAAAAAGGGGAGGTGTAAAAAAACCCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGTGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCATGACAGACAAAACGCAGCACAAGGGGGCCCAAAGCCAGGAGGAAGCTGTACTCTCGTTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAAAACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/datasets/all/tree.json b/nextclade/datasets/all/tree.json index 05066e2b..617ccca6 100644 --- a/nextclade/datasets/all/tree.json +++ b/nextclade/datasets/all/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Real-time tracking of dengue virus evolution", "updated": "2024-05-25", "build_url": "https://github.com/nextstrain/dengue", "maintainers": [{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": true, "color_by": "clade_membership"}, "genome_annotations": {"nuc": {"end": 10649, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/config/reference_all_genome.gb"}, "2K": {"end": 6827, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 6759, "strand": "+", "type": "CDS"}, "C": {"end": 440, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 102, "strand": "+", "type": "CDS"}, "E": {"end": 2423, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 939, "strand": "+", "type": "CDS"}, "M": {"end": 938, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 441, "strand": "+", "type": "CDS"}, "NS1": {"end": 3479, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 2424, "strand": "+", "type": "CDS"}, "NS2A": {"end": 4133, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 3480, "strand": "+", "type": "CDS"}, "NS2B": {"end": 4523, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 4134, "strand": "+", "type": "CDS"}, "NS3": {"end": 6377, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 4524, "strand": "+", "type": "CDS"}, "NS4A": {"end": 6758, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 6378, "strand": "+", "type": "CDS"}, "NS4B": {"end": 7562, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 6828, "strand": "+", "type": "CDS"}, "NS5": {"end": 10262, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 7563, "strand": "+", "type": "CDS"}, "pr": {"end": 713, "seqid": "../phylogenetic/config/reference_all_genome.gb", "start": 441, "strand": "+", "type": "CDS"}}, "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Israel", "#5E1D9D"], ["United Arab Emirates", "#4D22AE"], ["Pakistan", "#4B26B1"], ["India", "#472DB8"], ["Sri Lanka", "#4531BC"], ["Nepal", "#4335BF"], ["Bangladesh", "#4138C3"], ["Myanmar", "#403CC5"], ["Thailand", "#4041C7"], ["Malaysia", "#3F45C8"], ["Laos", "#3F4ACA"], ["Singapore", "#3F4ECB"], ["China", "#3F53CD"], ["Cambodia", "#3E58CF"], ["Vietnam", "#3E5CD0"], ["Indonesia", "#3F60D0"], ["Taiwan", "#4069CF"], ["Philippines", "#416DCE"], ["French Polynesia", "#447DCC"], ["Palau", "#4681CA"], ["Australia", "#4784C8"], ["Papua New Guinea", "#4887C6"], ["Kiribati", "#4F97BA"], ["Fiji", "#5199B7"], ["Gambia", "#539CB4"], ["Senegal", "#559EB1"], ["Guinea", "#57A0AE"], ["Mauritania", "#58A3AB"], ["C\u00f4te d'Ivoire", "#5AA5A7"], ["Burkina Faso", "#61AA9D"], ["Benin", "#68AF93"], ["Nigeria", "#6AB18F"], ["Niger", "#6CB28C"], ["Gabon", "#72B485"], ["Cameroon", "#74B582"], ["Republic of the Congo", "#77B67E"], ["Angola", "#7AB77B"], ["Democratic Republic of the Congo", "#7DB878"], ["Mozambique", "#89BB6B"], ["Tanzania", "#8CBB69"], ["Kenya", "#8FBC66"], ["Djibouti", "#95BD60"], ["Union of the Comoros", "#98BD5E"], ["Somalia", "#9FBE59"], ["Seychelles", "#A2BE57"], ["United Kingdom", "#AFBD4F"], ["France", "#B2BD4D"], ["Germany", "#B8BC4A"], ["Argentina", "#CAB843"], ["Paraguay", "#D1B340"], ["Bolivia", "#D4B13F"], ["Brazil", "#D6B03F"], ["Peru", "#D8AE3E"], ["Ecuador", "#DBAC3D"], ["Colombia", "#DDAA3C"], ["Guyana", "#DFA43B"], ["Venezuela", "#E0A13A"], ["Trinidad and Tobago", "#E29E39"], ["Grenada", "#E69237"], ["Nicaragua", "#E68D36"], ["El Salvador", "#E68033"], ["Saint Lucia", "#E67C33"], ["Honduras", "#E67832"], ["Dominica", "#E67431"], ["Guatemala", "#E56E30"], ["Guadeloupe", "#E5692F"], ["Saint Martin", "#E04E2A"], ["Jamaica", "#E04929"], ["Dominican Republic", "#DF4328"], ["Haiti", "#DE3E27"], ["Mexico", "#DE3826"], ["Cuba", "#DD3325"], ["Bahamas", "#DC2D24"], ["USA", "#DB2823"]]}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["Asia", "#447CCD"], ["Oceania", "#5EA9A1"], ["Africa", "#8ABB6A"], ["Europe", "#BEBB48"], ["South America", "#E29E39"], ["North America", "#E2562B"]]}, {"key": "genotype_nextclade", "title": "Dengue Genotype (Nextclade)", "type": "categorical", "scale": [["DENV1/I", "#5E1D9D"], ["DENV1/II", "#472DB8"], ["DENV1/III", "#3F48C9"], ["DENV1/IV", "#4066CF"], ["DENV1/V", "#4682C9"], ["DENV2/AA", "#5097BA"], ["DENV2/AI", "#5CA7A5"], ["DENV2/AII", "#6CB28D"], ["DENV2/AM", "#7FB976"], ["DENV2/C", "#93BD62"], ["DENV2/S", "#A9BD53"], ["DENV3/I", "#BFBB48"], ["DENV3/II", 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E349D, F354Y, N378S, R381K, I399L, N400T, K418R, E420G, M447I, L451P, K466A, K467Q, N469D, I473V, Y474F, M475S, E477D, N499Y, E510G, E517Q, Y523F, A529Q, A547S, E553A, K556S, T558K, R561E, D565T, K584R, R588K, R594K, T600V, S602A, L605M, E609D, A615S; NS4A: L6I, M7L, G11A, R12S, T18S, H19S, R22K, N23L, L28I, K42Q, T51S, F55L, L58V, A62G, G66A, L72F, *74Q, M81L, C87A, M89A, A90V, M97I, H103Q; NS4B: L6I, K11T, L13F, L15F, G16Y, N17Q, T19K, I22T, N23T, I45L, S56T, V60L, T63A, S82H, K83R, I86L, I102T, A107S, L109V, L110M, V112L, A113V, D153E, P156S, A176G, L187F, A190V, S199L, K208R, M218T, I236L, M237I, G241Q, S242T, A243P; NS5: I5T, P19S, G21D, I27E, K30R, E43S, G44A, R47D, E49S, T50K, T51I, H52K, A60S, L62I, F65I, N69G, E74K, C91M, G93T, S117A, Q127H, T128S, F134Y, T135K, P137T, K139Q, C140V, P152S, V156I, K173S, K174S, N175K, T176P, Q177E, K193E, I204S, N208C, N223G, M234T, R237K, M245T, N264S, A266S, I267T, T271K, N273D, D275T, K279R, I281L, E282Q, K283R, I284L, K285Q, T290E, D297E, 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"AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAGTTCTAACAGTTTGTTTGAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGGTGGTTAGACCACCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAGGGTTGGTGAAGAGATTCTCAACCGGACTTTTTTCTGGGAAAGGACCCTTACGGATGGTGCTAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAGAGATGGGGACAGTTGAAGAAAAATAAGGCCATCAAGATACTGATTGGATTCAGGAAGGAGATAGGCCGCATGCTGAACATCTTGAACGGGAGAAAAAGGTCAACGATAACATTGCTGTGCTTGATTCCCACCGTAATGGCGTTTTCCCTCAGCACAAGAGATGGCGAACCCCTCATGATAGTGGCAAAACATGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAATGCACTCTCATTGCCATGGACTTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCCCCCTACTGGTCAATACCGAACCTGAAGACATTGATTGCTGGTGCAACCTCACGTCTACCTGGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAGCTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGGATGTCATCGGAAGGGGCTTGGAAGCATGCTCAGAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCGCGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCTTCTTTGTCCTAATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTTAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCGAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCAGACATGGGTTGTGTGGCGTCATGGAGTGGGAAAGAATTGAAGTGTGGAAGCGGAATTTTTGTGGTTGACAACGTGCACACTTGGACAGAACAGTACAAATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCTGCAATATTAAATGCCCACAAAGATGGGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAGCAAATAACCAACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTAGTGGCTGGGGATGTGAAGGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCCCCAGTGAGTGATCTGAAATATTCATGGAAGACATGGGGAAAAGCAAAAATCTTCACCCCAGAAGCAAGAAATAGCACATTTTTAATAGACGGACCAGACACCTCTGAATGCCCCAATGAACGAAGAGCATGGAACTCTCTTGAGGTGGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTCCGAGAAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCTGCAATTAAAGATCAGAAAGCTGTGCATGCTGACATGGGTTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAGAGAAAGCATCTCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACCCACACACTGTGGAGCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAATCATATGCGGGCCCTTTTTCACAGCACAATTACCGCCAGGGCTATGCCACGCAAACCGTGGGCCCATGGCACTTAGGCAAATTAGAGATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACCATAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAACTAGTCACGCAATGGTGCTGCCGCTCCTGCACGATGCCTCCCTTAAGGTTCTTGGGAGAAGATGGGTGCTGGTATGGGATGGAGATTAGGCCCTTGAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGACGGCCGGACAGGGCACATCAGAAACTTTTTCTATGGGTCTGTTGTGCCTGACCTTGTTTGTGGAAGAATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTAGTTGTGGTGATCACTCTTTGTGCTATCATCCTGGGAGGCCTCACATGGATGGACTTACTACGAGCCCTCATCATGTTGGGGGACACTATGTCTGGTAGAATAGGAGGACAGATCCACCTAGCCATCATGGCAGTGTTCAAGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAGCACTAATGGTAATAGGAATGGCCATGACAACGGTGCTTTCAATTCCACATGACCTTATGGAACTCATTGATGGAATATCACTGGGACTAATTTTGCTAAAAATAGTAACACAGTTTGACAACACCCAAGTGGGAACCTTAGCTCTTTCCTTGACTTTCATAAGATCAACAATGCCATTGGTCATGGCTTGGAGGACCATTATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTGTGCAGGACAAGCTGTCTTCAAAAACAGTCTCATTGGGTAGAAATAACAGCACTCATCCTAGGAGCCCAAGCTCTGCCAGTGTACCTAATGACTCTTATGAAAGGAGCCTCAAGAAGATCTTGGCCTCTTAACGAGGGCATAATGGCTGTGGGTTTGGTTAGTCTCTTAGGAAGCGCTCTTTTAAAGAATGATGTCCCTTTAGCTGGCCCAATGGTGGCAGGAGGCTTACTTCTGGCGGCTTACGTGATGAGTGGTAGCTCAGCAGATCTGTCACTAGAGAAGGCCGCCAACGTGCAGTGGGATGAAATGGCAGACATAACAGGCTCAAGCCCAATCGTAGAAGTGAAGCAGGATGAAGATGGCTCTTTCTCCATACGGGACGTCGAGGAAACCAATATGATAACCCTTTTGGTGAAACTGGCACTGATAACAGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACCTTATGGTACATGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTCCCCTCACCCGCTGCCACTAAAAAAGCCGCACTGTCTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTATTCGGGAAAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAACAAGAGGATCAGTGATCTGCCACGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCAGGAATGACATGATATCATACGGTGGGGGATGGAGGCTTGGAGACAAATGGGACAAAGAAGAAGACGTTCAGGTCCTCGCCATAGAACCAGGAAAAAATCCTAAACATGTCCAAACGAAACCTGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTAGATTTCAAACCCGGAACGTCTGGTTCTCCCATCATCAACAGGAAAGGAAAAGTCATCGGACTCTATGGAAATGGAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGAGAGCCAGATTATGAAGTGGATGAGGACATTTTTCGAAAGAAAAGATTAACTATAATGGACTTACACCCCGGAGCTGGAAAGACAAAAAGAATTCTTCCATCAATAGTGAGAGAAGCCTTAAAAAGGAGGCTACGAACTTTGATTTTAGCTCCCACGAGAGTGGTGGCGGCCGAGATGGAAGAGGCCCTACGTGGACTGCCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAGGAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTTTTGTCATCAACCAGGGTTCCAAATTACAACCTTATAGTGATGGATGAAGCACATTTCACCGATCCTTCTAGTGTCGCGGCTAGAGGATACATCTCGACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCTTCATGACCGCAACCCCTCCCGGAGCGACAGATCCCTTTCCCCAGAGCAACAGCCCAATAGAAGACATCGAGAGGGAAATTCCGGAAAGGTCATGGAACACAGGGTTCGACTGGATAACAGACTACCAAGGGAAAACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAAATTGTTTGAGAAAGTCGGGAAAGAAAGTTATCCAGTTGAGTAGGAAAACCTTTGATACAGAGTATCCAAAAACGAAACTCACGGACTGGGACTTTGTGGTCACTACAGACATATCTGAAATGGGGGCCAATTTTAGAGCCGGGAGAGTGATAGACCCTAGAAGATGCCTCAAGCCAGTTATCCTACCAGATGGGCCAGAGAGAGTCATTTTAGCAGGTCCTATTCCAGTGACTCCAGCAAGCGCTGCTCAGAGAAGAGGGCGAATAGGAAGGAACCCAGCACAAGAAGACGACCAATACGTTTTCTCCGGAGACCCACTAAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGATGCTGCTTGACAATATCTACACCCCAGAAGGGATCATTCCAACATTGTTTGGTCCGGAAAGGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTTTTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCTGCTGGCATTTCTTACGAAGATCGGGAATGGTGCTTCACAGGGGAAAGAAATAACCAAATTTTAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAGCTAAGGCCAAGATGGTTAGATGCACGTGTATACGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGTTTGCCAGTGGAAGGAAGAGTATAACTCTCGACATCCTAACAGAGATTGCCAGTTTGCCAACTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGATAACATAGTCATGCTCCACACAACAGAAAGAGGAGGGAGGGCCTATCAACACGCCCTGAACGAACTTCCGGAGTCACTGGAAACACTCATGCTTGTAGCTTTACTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTCATGCAAGGGAAAGGAATAGGGAAATTGTCAATGGGTTTGATAACCATTGCGGTGGCTAGTGGCTTGCTCTGGGTAGCAGAAATTCAACCCCAGTGGATAGCGGCCTCAATCATACTAGAGTTTTTTCTCATGGTACTGTTGATACCGGAACCAGAAAAACAAAGGACCCCACAAGACAATCAATTGATCTACGTCATATTGACCATTCTCACCATCATTGGTCTAATAGCAGCCAACGAGATGGGGCTGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCCTCGATGTGGACTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACAATTCTGACTCCCATGCTGAGACACACCATAGAAAACACGTCGGCCAACCTATCTCTAGCAGCCATTGCCAACCAGGCAGCCGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGGACCTCGGTGTGCCGCTGTTAGCAATGGGATGCTATTCTCAAGTGAACCCAACAACCTTGACAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGCCCAGGATTGCAGGCAAAAGCCACAAGAGAGGCCCAGAAAAGGACAGCTGCTGGGATCATGAAAAATCCCACAGTGGACGGGATAACAGTAATAGATCTAGAACCAATATCCTATGACCCAAAATTTGAAAAGCAATTAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACATGGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAATCTTGACCTTGTGGGAGGGCAACCCGGGAAGGTTTTGGAACACGACCATAGCCGTATCCACCGCCAACATTTTCAGGGGAAGTTACTTGGCGGGAGCTGGACTGGCTTTTTCACTCATAAAGAATGCACAAACCCCTAGGAGGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCATTAGACAGAAAAGAGTTTGAAGAGTATAAAAGAAGTGGAATACTAGAAGTGGACAGGACTGAAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTATCAAGAGGGTCCAGTAAGATCAGATGGATTGTTGAGAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTAGATCTTGGCTGTGGGAGAGGAGGATGGTCTTATTACATGGCGACACTCAAGAACGTGACTGAAGTGAAAGGGTATACAAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACTTATGGTTGGAATTTGGTCAAACTCCATTCAGGGGTTGACGTGTTCTACAAACCCACAGAGCAAGTGGACACCCTGCTCTGTGATATTGGGGAGTCATCTTCTAATCCAACAATAGAGGAAGGAAGAACATTAAGAGTTTTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCATCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAGCTGGAGAAACTGCAGAGAAAACATGGTGGGAACCTTGTCAGATGCCCGCTGTCCAGGAACTCCACCCATGAGATGTATTGGGTGTCAGGAGCGTCGGGAAACATTGTGAGCTCTGTGAACACAACATCAAAGATGTTGTTGAACAGGTTCACAACAAGGCATAGGAAACCCACTTATGAGAAGGACGTAGATCTTGGGGCAGGAACGAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAAGGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACCTGGCATTATGATCAGGAAAACCCATACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCTGCATCCTCCATGGTGAACGGGGTGGTAAAACTGCTAACAAAACCCTGGGATGTGATTCCAATGGTGACTCAGTTAGCCATGACAGATACAACCCCTTTTGGGCAACAAAGAGTGTTCAAAGAGAAGGTGGATACCAGAACACCACAACCAAAACCCGGTACACGAATGGTTATGACCACGACAGCCAATTGGCTGTGGGCCCTCCTTGGAAAGAAGAAAAATCCCAGACTGTGCACAAGGGAAGAGTTCATCTCAAAAGTTAGATCAAACGCAGCCATAGGCGCAGTCTTTCAGGAAGAACAGGGATGGACATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGGCCCTACACCAGGAAGGGAAATGTGAATCGTGTGTCTATAACATGATGGGAAAACGTGAGAAAAAGTTAGGAGAGTTTGGCAGAGCCAAGGGAAGCCGAGCAATCTGGTACATGTGGCTGGGAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTTTTGAATGAAGATCACTGGTTTGGCAGAGAAAATTCATGGAGTGGAGTGGAAGGGGAAGGTCTGCACAGATTGGGATATATCCTGGAGGAGATAGACAAGAAGGATGGAGACCTAATGTATGCTGATGACACAGCAGGCTGGGACACAAGAATCACTGAGGATGACCTTCAAAATGAGGAACTGATCACGGAACAGATGGCTCCCCACCACAAGATCCTAGCCAAAGCCATTTTCAAACTAACCTATCAAAACAAAGTGGTGAAAGTCCTCAGACCCACACCGCGGGGAGCGGTGATGGATATCATATCCAGGAAAGACCAAAGAGGTAGTGGACAAGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTTCAACTCATCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGTTGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTAAAGAGGATGGCAATCAGTGGAGACGATTGCGTGGTGAAGCCCCTAGATGAGAGGTTTGGCACTTCCCTCCTCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCTAAGGGATGGAAAAACTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTTATGAAGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCAGAATCTCGCAGGGAGCTGGATGGAGCTTAAGAGAAACAGCCTGCCTGGGCAAAGCTTACGCCCAGATGTGGTCGCTTATGTACTTCCACAGAAGGGATCTGCGTTTAGCCTCCATGGCCATATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACGCTCATCACCAGTGGATGACCACTGAAGATATGCTCAAAGTGTGGAACAGAGTGTGGATAGAAGACAACCCTAATATGACTGACAAGACTCCAGTCCATTCGTGGGAAGATATACCTTACCTAGGGAAAAGAGAGGATTTGTGGTGTGGATCCCTGATTGGACTTTCTTCCAGAGCCACCTGGGCGAAGAACATTCATACGGCCATAACCCAGGTCAGGAACCTGATCGGAAAAGAGGAATACGTGGATTACATGCCAGTAATGAAAAGATACAGTGCTCCTTCAGAGAGTGAAGGAGTTCTGTAATTACCAACAACAAACACCAAAGGCTATTGAAGTCAGGCCACTTGTGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAATGGGAGGCGTAATAATCCCCAGGGAGGCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCTCCCATCACTGATAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTGGTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGATGGATTGGTGTTGTTGATCCAACAGGTTCT", "2K": "TPQDNQLIYVILTILTIIGLIAA", "C": "MNQRKKVVRPPFNMLKRERNRVSTPQGLVKRFSTGLFSGKGPLRMVLAFITFLRVLSIPPTAGILKRWGQLKKNKAIKILIGFRKEIGRMLNILNGRKRSTITLLCLIPTVMA", "E": "MRCVGVGNRDFVEGVSGGAWVDLVLEHGGCVTTMAQGKPTLDFELTKTTAKEVALLRTYCIEASISNITTATRCPTQGEPYLKEEQDQQYICRRDVVDRGWGNGCGLFGKGGVVTCAKFSCSGKITGNLVQIENLEYTVVVTVHNGDTHAVGNDTSNHGVTAMITPRSPSVEVKLPDYGELTLDCEPRSGIDFNEMILMKMKKKTWLVHKQWFLDLPLPWTAGADTSEVHWNYKERMVTFKVPHAKRQDVTVLGSQEGAMHSALAGATEVDSGDGNHMFAGHLKCKVRMEKLRIKGMSYTMCSGKFSIDKEMAETQHGTTVVKVKYEGAGAPCKVPIEIRDVNKEKVVGRIISSTPLAENTNSVTNIELEPPFGDSYIVIGVGNSALTLHWFRKGSSIGKMFESTYRGAKRMAILGETAWDFGSVGGLFTSLGKAVHQVFGSVYTTMFGGVSWMIRILIGFLVLWIGTNSRNTSMAMTCIAVGGITLFLGFTVQA", "M": "FSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVTYKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSGMGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQRTVFFVLMMLVAPSYG", "NS1": "DMGCVASWSGKELKCGSGIFVVDNVHTWTEQYKFQPESPARLASAILNAHKDGVCGIRSTTRLENVMWKQITNELNYVLWEGGHDLTVVAGDVKGVLTKGKRALTPPVSDLKYSWKTWGKAKIFTPEARNSTFLIDGPDTSECPNERRAWNSLEVEDYGFGMFTTNIWMKFREGSSEVCDHRLMSAAIKDQKAVHADMGYWIESSKNQTWQIEKASLIEVKTCLWPKTHTLWSNGVLESQMLIPKSYAGPFSQHNYRQGYATQTVGPWHLGKLEIDFGECPGTTVTIQEDCDHRGPSLRTTTASGKLVTQWCCRSCTMPPLRFLGEDGCWYGMEIRPLSEKEENMVKSQVTA", "NS2A": "GQGTSETFSMGLLCLTLFVEECLRRRVTRKHMILVVVITLCAIILGGLTWMDLLRALIMLGDTMSGRIGGQIHLAIMAVFKMSPGYVLGVFLRKLTSRETALMVIGMAMTTVLSIPHDLMELIDGISLGLILLKIVTQFDNTQVGTLALSLTFIRSTMPLVMAWRTIMAVLFVVTLIPLCRTSCLQKQSHWVEITALILGAQALPVYLMTLMKGASRR", "NS2B": "SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSADLSLEKAANVQWDEMADITGSSPIVEVKQDEDGSFSIRDVEETNMITLLVKLALITVSGLYPLAIPVTMTLWYMWQVKTQR", "NS3": "SGALWDVPSPAATKKAALSEGVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMISYGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTSGSPIINRKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPSSVAARGYISTRVEMGEAAAIFMTATPPGATDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILPDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYEDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPRWLDARVYADPMALKDFKEFASGRK", "NS4A": "SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPESLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEIQPQWIAASIILEFFLMVLLIPEPEKQR", "NS4B": "NEMGLIEKTKTDFGFYQVKTETTILDVDLRPASAWTLYAVATTILTPMLRHTIENTSANLSLAAIANQAAVLMGLGKGWPLHRMDLGVPLLAMGCYSQVNPTTLTASLVMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYDPKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPILTLWEGNPGRFWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRR", "NS5": "GTGTTGETLGEKWKRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSSKIRWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGPGHEEPIPMATYGWNLVKLHSGVDVFYKPTEQVDTLLCDIGESSSNPTIEEGRTLRVLKMVEPWLSSKPEFCIKVLNPYMPTVIEELEKLQRKHGGNLVRCPLSRNSTHEMYWVSGASGNIVSSVNTTSKMLLNRFTTRHRKPTYEKDVDLGAGTRSVSTETEKPDMTIIGRRLQRLQEEHKETWHYDQENPYRTWAYHGSYEAPSTGSASSMVNGVVKLLTKPWDVIPMVTQLAMTDTTPFGQQRVFKEKVDTRTPQPKPGTRMVMTTTANWLWALLGKKKNPRLCTREEFISKVRSNAAIGAVFQEEQGWTSASEAVNDSRFWELVDKERALHQEGKCESCVYNMMGKREKKLGEFGRAKGSRAIWYMWLGARFLEFEALGFLNEDHWFGRENSWSGVEGEGLHRLGYILEEIDKKDGDLMYADDTAGWDTRITEDDLQNEELITEQMAPHHKILAKAIFKLTYQNKVVKVLRPTPRGAVMDIISRKDQRGSGQVGTYGLNTFTNMEVQLIRQMEAEGVITQDDMQNPKGLKERVEKWLKECGVDRLKRMAISGDDCVVKPLDERFGTSLLFLNDMGKVRKDIPQWEPSKGWKNWQEVPFCSHHFHKIFMKDGRSLVVPCRNQDELIGRARISQGAGWSLRETACLGKAYAQMWSLMYFHRRDLRLASMAICSAVPTEWFPTSRTTWSIHAHHQWMTTEDMLKVWNRVWIEDNPNMTDKTPVHSWEDIPYLGKREDLWCGSLIGLSSRATWAKNIHTAITQVRNLIGKEEYVDYMPVMKRYSAPSESEGVL", "pr": "FSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVTYKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKR"}} \ No newline at end of file +{"version": "v2", "meta": {"title": "Real-time tracking of dengue virus evolution", "updated": "2024-05-31", "build_url": "https://github.com/nextstrain/dengue", "maintainers": [{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": true, "color_by": "clade_membership"}, "genome_annotations": {"nuc": {"end": 10649, "start": 1, "strand": "+", "type": "##sequence-region pragma", "seqid": "resources/all/genome_annotation.gff3"}, "2K": {"end": 6827, "seqid": "resources/all/genome_annotation.gff3", "start": 6759, "strand": "+", "type": "gene"}, "C": {"end": 440, "seqid": "resources/all/genome_annotation.gff3", "start": 102, "strand": "+", "type": "gene"}, "E": {"end": 2423, "seqid": "resources/all/genome_annotation.gff3", "start": 939, "strand": "+", "type": "gene"}, "M": {"end": 938, "seqid": 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Y323F, I324L, N339S, L345M, L349Q, T351A; NS2A: H2Q, K4T, V5S, D6E, N7T, I10M, M15L, A16T, V22C, T25R, G28T, V38A, F40L, V41C, T42A, L43I, T45L, N47G, M48L, R51M, V56A, V60L, A62D, D66G, V71Q, T72I, Y73H, L76I, A79V, R83S, I85G, F86Y, A87V, V88L, L90V, I100T, I101A, T104V, S112H, G113D, I115V, D117H, A118D, I119L, V120M, T123I, I130L, M131I, V132L, E140D, K141N, Y142T, A146T, T147L, I148A, C153F, T159P, H161I, N162M, K165R, T168M, I169V, I170V, A172F, S175T, F177I, L181R, S184C, T189S, D190H, I192V, P193E, L196A, T197I, I199L, V201A, K202Q, P203A, M206V, F207Y, I209M, T212M, T214G, S215A, K216S; NS2B: M13L, I16L, A18G, S20A, M28L, L32M, I39L, C41A, I44M, T45S, D58N, K60Q, E62D, E64M, E66D, S68T, A70S, L75E, T77K, V78Q, E79D, T83S, M84F, K87R, E89V, E92T, T94M, L95I, I97L, I99V, T101L, L104I, V105T, F110Y, S113A, V120L, M126V, K128T; NS3: V3A, P11A, V13A, E14Q, E17T, E19T, D20E, K26M, I30L, S34T, Y41H, K42M, A56S, L58I, M59C, K61E, G62T, K63G, K73R, K74N, L76M, E86G, G87E, K90D, G92E, 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{"value": "denv1", "confidence": {"denv1": 1.0}, "entropy": -1.000088900581841e-12}, "region": {"value": "South America", "confidence": {"South America": 1.0}, "entropy": -1.000088900581841e-12}, "genotype_nextclade": {"value": "DENV1/V", "confidence": {"DENV1/V": 1.0}, "entropy": -1.000088900581841e-12}}, "branch_attrs": {"mutations": {"nuc": ["C3152T", "T3962C", "G6569A"]}}}, {"name": "DENV-1/TO-UFT-112972", "node_attrs": {"div": 2758, "genbank_accession": {"value": "OR518247"}, "author": {"author": "Souza,U.J.B.,Macedo,Y.S.M.,Santos,R.N.,Cardoso,F.D.P.,Galvao,J.D.,Gabev,E.E.,Franco,A.C.,Roehe,P.M.,Spilki,F.R.,Campos,F.S.", "value": "Souza,U.J.B.,Macedo,Y.S.M.,Santos,R.N.,Cardoso,F.D.P.,Galvao,J.D.,Gabev,E.E.,Franco,A.C.,Roehe,P.M.,Spilki,F.R.,Campos,F.S."}, "clade_membership": {"value": "DENV1"}, "country": {"value": "Brazil"}, "serotype_genbank": {"value": "denv1", "confidence": {"denv1": 1.0}, "entropy": -1.000088900581841e-12}, "region": {"value": "South America", "confidence": {"South America": 1.0}, "entropy": -1.000088900581841e-12}, "genotype_nextclade": {"value": "DENV1/V", "confidence": {"DENV1/V": 0.9999999999999999}, "entropy": -9.99866855976916e-13}}, "branch_attrs": {"mutations": {"nuc": ["A423C", "C2498T", "G2900A", "T3716C", "T4103A", "T4547C", "A4556G", "T5009C", "A7187T", "C7646T", "C7842T", "T8480C", "G9140A", "A9167G", "G9656A"], "C": ["M108L"]}, "labels": {"aa": "C: M108L"}}}]}, {"name": "NODE_0001507", "node_attrs": {"div": 2736, "clade_membership": {"value": "DENV1"}, "serotype_genbank": {"value": "denv1", "confidence": {"denv1": 0.9999999979139966}, "entropy": 4.6389850677035856e-08}, "region": {"value": "South America", "confidence": {"South America": 0.9995430302833479}, "entropy": 0.004032013285097307}, "genotype_nextclade": {"value": "DENV1/V", "confidence": {"DENV1/V": 0.9999999877446754}, "entropy": 2.6607101900823855e-07}}, "branch_attrs": {"mutations": {"nuc": ["A1415G", "T1420C", "T1559A", "C2498T", "T7361C", "T9164C"], "E": ["I161T"]}, "labels": {"aa": "E: I161T"}}, "children": [{"name": "DENV-1/Brazil/TO-UFT-4547", "node_attrs": {"div": 2765, "genbank_accession": {"value": "OR518272"}, "author": {"author": "Souza,U.J.B.,Macedo,Y.S.M.,Santos,R.N.,Cardoso,F.D.P.,Galvao,J.D.,Gabev,E.E.,Franco,A.C.,Roehe,P.M.,Spilki,F.R.,Campos,F.S.", "value": "Souza,U.J.B.,Macedo,Y.S.M.,Santos,R.N.,Cardoso,F.D.P.,Galvao,J.D.,Gabev,E.E.,Franco,A.C.,Roehe,P.M.,Spilki,F.R.,Campos,F.S."}, "clade_membership": {"value": "DENV1"}, "country": {"value": "Brazil"}, "serotype_genbank": {"value": "denv1", "confidence": {"denv1": 0.9999999999999999}, "entropy": -9.99866855976916e-13}, "region": {"value": "South America", "confidence": {"South America": 1.0}, "entropy": -1.000088900581841e-12}, "genotype_nextclade": {"value": "DENV1/V", "confidence": {"DENV1/V": 1.0}, "entropy": -1.000088900581841e-12}}, "branch_attrs": {"mutations": {"nuc": ["A605G", "T869C", "G1823A", "C1883T", "C2411T", "G2432A", "A2723G", "T3095C", "G3116A", "A4457G", "T4847C", "T5753C", "T6399C", "C6473T", "A6842G", "T6843C", "C7004T", "A7187T", "T7502C", "C7663T", "C8186T", "C8192T", "G8255A", "C8786T", "G9302A", "A9305G", "T9653C", "G9656A", "T10504C"], "NS5": ["T34M"]}, "labels": {"aa": "NS5: T34M"}}}, {"name": "DENV-1/Brazil/TO-UFT-417", "node_attrs": {"div": 2751, "genbank_accession": {"value": "OR518270"}, "author": {"author": "Souza,U.J.B.,Macedo,Y.S.M.,Santos,R.N.,Cardoso,F.D.P.,Galvao,J.D.,Gabev,E.E.,Franco,A.C.,Roehe,P.M.,Spilki,F.R.,Campos,F.S.", "value": "Souza,U.J.B.,Macedo,Y.S.M.,Santos,R.N.,Cardoso,F.D.P.,Galvao,J.D.,Gabev,E.E.,Franco,A.C.,Roehe,P.M.,Spilki,F.R.,Campos,F.S."}, "clade_membership": {"value": "DENV1"}, "country": {"value": "Brazil"}, "serotype_genbank": {"value": "denv1", "confidence": {"denv1": 1.0}, "entropy": -1.000088900581841e-12}, "region": {"value": "South America", "confidence": {"South America": 0.9999999999999999}, "entropy": -9.99866855976916e-13}, "genotype_nextclade": {"value": "DENV1/V", "confidence": {"DENV1/V": 1.0}, "entropy": -1.000088900581841e-12}}, "branch_attrs": {"mutations": {"nuc": ["G531A", "C852T", "C1311T", "G1952A", "G2119A", "G2969A", "A3266G", "T4181C", "T4736C", "A5711G", "A6947G", "G9162T", "C9548T", "T9557C", "G10486A"], "E": ["R394K"], "M": ["V31I", "L138F"], "NS5": ["D534Y"], "pr": ["V31I"]}, "labels": {"aa": "E: R394K; M: V31I, L138F; NS5: D534Y; pr: V31I"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}, "root_sequence": {"nuc": "AGTTGTTAGTCTACGTGGACCGACAAGGACAGTTTCGAATCGGAAGCTTGCTTAACGTAGTTCTAACAGTTTTTTTAATTAGAGAGCAGATCTCTGAGATGAACAACCAACGGAAAAAGGCGGGAAAACCGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCAACTGTACAACAGTTGGCGAAGAGATTCTCAATAGGATTGCTGTAAGGGCAAGGACCATTAAAATTGGTTATGGCTTTCATAGCATTCCTACGATTCCTAGCCATCCCACCAACAGCAGGGATTTTGAAAAGATGGGGAACATTCAAGAAGTCTAAGGCTATCAAGGTACTGAGAGGATTCAGGAAGGAGATCGGAAGCATGCTGAACATTTTGAACAGGAGAAAAAGAACAGCAATCATTCTCATGATGCTGATTCCAACAGTAATGGCGTTCCATTTGACCACACGAGATGGAGAGCCGCACATGATTGTGAGCAAGCATGAAAGAGGAAAATCCCTTCTGTTTAAGACAGCGGATGGAATCAACATGTGCACCCTCATTGCCATGGATCTGGGTGAGTTGTGTGAGGACACAATCACGTACAAATGCCCCCTTCTCACCGAAACCGAACCAGAAGACATTGACTGCTGGTGCAATCCCACGTCCACATGGGTGACCTATGGGACGTGTACCCAAACTGGAGAACACAGACGAGAGAAAAGATCAGTGGCACTAGCCCCACATGTGGGAATGGGACTGGAAACAAGAACTGAAACATGGATGTCATCAGAAGGAGCTTGGAAACAAGCCCAGAGAGTAGAGACTTGGATTCTGAGACACCCAGGATTCACGATAATGGCAGTATTTCTGGCATACACCATAGGAACAACATATATCCAGAGAGTCGTTATTTTTATCCTACTGATGCTGGTCGCCCCATCCATGACAATGCGATGCGTGGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTTTCAGGAGGAACGTGGGTTGACGTGGTGCTAGAACATGGAAGTTGTGTCACAACCATGGCAAAGAACAAACCAACACTGGACTTTGAACTGATGAAGACAGAAGCCAAACAACCGGCCACACTAAGGAAATTCTGCATTGAAGCTAAAATAACCAACACAACAACAGAATCAAGATGTCCAACACAAGGGGAACCCAATCTAGTAGAGGAGCAGGACCAGAAGTTCGTCTGCAAACAAACGATGGTGGACAGAGGATGGGGCAATGGCTGTGGTTTGTTTGGAAAAGGAGGCATTGTGACATGTGCGAAGTTTACATGCTTGAAGAAAATAGAAGGAAAAGTGGTGCAACCTGAAAACTTAGAATACACCGTGGTCATAACAGTCCACACAGGAGACGAACACGCAGTGGGAAATGACACAACAAAACATGGAATGACGGCCAAGATAACACCCCAGGCTTCCACCGCAGAAGCTAAACTGACAGACTATGGAACTCTCACGCTGGATTGCTCACCAAGAACAGGTCTCGACTTTAATGAGATGGTCTTGTTGAAAATGAAAAACAAAGCATGGCTTGTACACAGACAATGGTTCCTAGACCTACCTCTACCATGGACATCAGGAGCTGACACATAAGAAGCAAATTGGAACCAGAAAGAGATGCTGGTGACATTCAAAAATCCTCATGCAAAGAAACAGGATGTAGTCGTCCTAGGATCCCAAGAAGGAGCCATGCACACAGCACTCACAGGAGCTACAGAAATCCAAACGTCAGGAGGAAACTTAATGTTTGCAGGACACCTGAAGTGCAGACTGAGAATGGACAAACTGAAACTCAAAGGGATGTCATACGCGATGTGCACAGGAAAGTTCAAAATTGAGAAAGAAATGGCAGAAACACAGCATGGAACAATAGTCATTAAGGTTAAGTATGAAGGAGATGGTGCACCATGCAAGATCCCTTTTGAGATAAAGGATGTGAAAAAGAAAAATGTCATTGGGCGACTGATCACAGCCAACCCAATAGTCACAGAGAAAGACAGTCCAGTCAACATTGAAGCAGAACCTCCTTTTGGGGACAGCTACATCGTGATAGGAGTAGGAGAAAGAGCATTGAAACTCAACTGGTTCAAGAAAGGAAGCTCCATTGGGAAAATGTTTGAGGCAACTGCCAGAGGAGCAAAAAGAATGGCCATCTTGGGAGACACAGCCTGGGATTTTGGATCTGTAGGAGGAGTGTTCACATCAGTAGGAAAGGCGGTGCACCAGGTTTTTGGAACTGTCTATGGGGCTATGTTTAGCGGAGTCTCATGGACCATGAAAATCCTAATAGGGGTTCTCATAACATGGATAGGAATGAATTCAAGAAGCACTTCCCTGTCAATGACATGCATAGCAGTAGGAATCGTCACACTGTACCTGGGAGTCATGGTGCAGGCGGACATGGGTTGTGTTGTGAACTGGAAAGGCAAAGAACTGAAATGTGGAAGTGGAATTTTTGTCACTGACAACGTGCACACTTGGACAGAACAATACAAATTCCAACCAGACTCCCCAACAAGACTGGCGTCAGCCATTCCGAAAGCTCATGAGGAGGGAGTCTGTGGAATCCGATCAGCAACAAGACTGGAGAATCTCATGTGGAAGCAAATAACAAATGAATTGAACCACATCCTATGGGAAAATGAAATCAAACTAACTGTAGTGGCAGGAGACATTAAAGGAATCTTGGAGAAAGGGAAAAGAACACTTACACCTCAACCCATTGAGCTGAAATATTCATGGAAAACATGGGGAAAAGCAAAAATACTCACAGCAGAAGTACAAAATAACACCTTCCTCATAGACGGTCCAGACACACCAGAATGCCCTAATGACCAAAGAGCATGGAATTTTCTGGAAGTTGAGGACTATGGATTTGGAATCTTCACGACCAACATATGGCTGAAATTGCGAGAAGAGTACACCGAAGTGTGTGACCACAGGCTAATGTCAGCAGCCATCAAGGACAACAGGGCCGTCCATGCTGACATGGGCTATTGGATAGAAAGCGCAAAGAATGAGACCTGGAAGATAGAGAAAGCATCCTTCATTGAAGTTAAAACCTGCCTCTGGCCAAAATCACACACTCTTTGGAGCAATGGAGTGCTAGAAAGTGAAATGATAATTCCAAAGATTTTTGCTGGACCAATTTCACAGCACAACTACAGACCAGGCTATTACACACAAACAGCAGGACCATGGCACTTAGGCAAATTGGAGATGGACTTTGATTTTTGTGAAGGAACCACAGTTGTAGTGACTGAGGACTGTGGAAATAGAGGCCCATCTTTGAGAACAACCACAGCCTCAGGAAAACTGATAACTGAATGGTGCTGCCGATCTTGCACATTACCTCCCCTAAGATACATAGGAGAGGATGGATGCTGGTATGGGATGGAAATCAGACCCTTGAATGAGAAAGAAGAGAACCTGGTCAAGTCATTGGTCACAGCCGGGCATGGAAAGGTGGACAATTTTTCAATAGGACTCTTGTGCATGGCATTGTTCATGGAAGAGGTGCTGAGAACCAGAGTTGGCAGAAAACACATGATATTAGTAGTAGTGGTTACCTTCGTGACCCTCATCACAGGGAATATGACATGGAGAGACCTGGTAAGAGTACTTATCATGGTGGGAGCCACTATGTCTGATAGAATGGGGGGCGTGACTTACCTAGCTTTAATGGCAGCTTTCAAAATGAGACCAATCTTCGCAGTGGGATTGTTCTTGAGGAAACTGACTTCAAGAGAAATAATACTGATGACAATAGGAATGGCCCTGGTAACATCGTTCCAAATACCAGATGCCATTGTGGAACTGACTGATGGAATAGCATTGGGGATAATGGTGCTTAAAATGGTGACACATTTTGAAAAATACCAGTTGGGAGCGACCATCCTGTCCTTGACGTGCATCAAAACAACTATGACATTGCATAATGCATGGAAAACAATCACCATTATATTGGCAGTAGTTTCTCTTTTCCCATTGTGCCTGACTTCCTCCCTTCAAAAACAGACAGATTGGATACCAATAACATTGACAATCATAGGAGTCAAACCACTACCCATGTTTCTAATAACTTTAACAAAAACCAGCAAAAAAAGAAGTTGGCCTCTCAATGAGGGCATTATGGCTGTTGGAATGGTGAGCATTCTAGCAAGTTCTCTCCTAAAGAATGATGTTCCCATGGCTGGACCATTAGTGGCTGGAGGCTTGCTCATAGCGTGCTACGTGATAACTGGCAGCTCAGCAGACTTGTCACTGGAGAAAGCCGCCGATGTGAAATGGGAAGAAGAGGCAGAGATATCAGGAGCCAGCCCAATCATATTAGTCACAGTAGAAGAAGATGGTACCATGTCAATAAAGGATGAAGAGGAAGAGAACACACTAACCATACTCATAAAAACAGCACTGCTAGTAGTGTCAGGCCTCTTCCCATTGTCAATACCAGTCACAATGGCGGTATGGTACATGTGGCAAATGAAAAAACAAAGATCCGGAGTGCTGTGGGACGTCCCCTCACCCCCAGCAGTGGAAAAAGCTGAACTGGAAGATGGAGTCTATAGAATCAAGCAAAGAGGGATTTTTGGGAAATCCCAAGTTGGAGTTGGAGTATACAAAGAAGGAGTATTCCACACAATGTGGCACGTCACAAGAGGAGCTGTCCTCATGCATAAAGGGAAGAGACTGGAACCATCTTGGGCTGACGTCAAGAAAGACTTGATATCATATGGAGGAGGTTGGAGGCTTGAAGGAAAATGGAAAAAAGGAGAAGAAGTGCAGGTCTTGGCCGTAGAACCTGGGAAAAATCCAAAAAACGTCCAAACAAAACCTGGCCTTTTCAAGACCACTACAGGAGAAATAGGAGCCGTAGCCCTGGACTTCAAACCTGGAACATCAGGATCTCCCATCATTAACAAAAAAGGAAAAGTTGTGGGTCTCTATGGAAATGGAGTGGTTACAAAAAGTGGAGCCTATGTCAGTGCCATAGCGCAAACTGAAAAAATTGAAGAGCCGAATCCAGAGATTGAAGATGACATCTTTAGAAAGAAAAGATTAACCATAATGGACCTACATCCAGGAGCGGGAAAGACAAAAAGATATCTCCCAGCCATAGTCAGAGAGGCCATAAAAAGAAGCCTGAGAACTCTAATCTTGGCTCCCACAAGAGTGGTGGCAGCTGAAATGGAAGAAGCCCTAAGAGGACTCCCAATAAGTTATCAGACCCCAGCCATGAAGGCTGAACACACAGGAAGGGAGATTGTAGACCTAATGTGCCATGCCACTTTCACCATGAGACTGCTGTCACCAATCAGGGTTCCAAATTACAACCTGATAATAATGGATGAAGCACATTTCACAGACCCAGCCAGCATAGCGGCTAGAGGATACATCTCAACCCGAGTGGAAATGGGAGAGGCAGCTGCAATTTTTATGACAGCCACTCCCCCAGGAACGACAGATCCCTTTCCTCAGAGCAACGCCCCAATCAAAGATGAAGAAAGAGAAATTCCTGAACGCTCATGGAATTCAGGATATGAATGGATCACAGATTTTCAAGGGAAGACAGTGTGGTTTGTTCCAAGCATAAAAGCCGGAAATGACATAGCAAACTGCTTGAGAAAAAATGGAAAAAGGGTGATTCAACTGAGTAGGAAAACCTTTGACACAGAATATCCAAAAACAAAAATCAATGACTGGGACTTTGTGGTCACAACAGACATTTCCGAAATGGGAGCCAATTTCAAAGCTGAGAGAGTGATAGACCCAAGGAGATGCCTGAAGCCAGTTATACTGACAGATGGTCCAGAGCGGGTGATTCTGGCAGGACCCATGCCAGTGACCCTAGCAAGTGCTGCCCAAAGAAGAGGGAGAATAGGAAGGAACCCAAAAAAAGAAAATGACCAGTACATTTACATGGGAGAGCCTCTAAAAAATGATGAAGACCATGCTCACTGGACAGAAGCAAAGATGCTCCTTGACAACATCAACACACCAGAAGGGATCATCCCAACCCTGTTTGAACCAGAAAGGGAAAAGACTGAAGCCATAGACGGTGAATACCGCCTGAGAGGGGAAGCAAGGAAAACCTTTGTGGAACTAATGAGAAGAGGAGACCTACCAGTTTGGCTGGCCTACAAAGTAGCTTCAGAAGGCATCAAATACACAGACAGAAGGTGGTGCTTTGATGGAGAAAGGAACAATCAAATTTTGGAGGAGAACATGGAAGTGGAAATCTGGACAAAAGAAGGAGAAAGGAAGAAATTAAGACCTAGATGGTTGGATGCTAGAACTTATTCTGACCCACTGGCACTAAAGGAATTCAAGGAGTTTGCAGCTGGAAGAAAGTCCATAACCCTTGACCTAATAACAGAAATAGGTAGACTGCCAACTTACTTGACCCACAGGGCCAGAAATGCCCTGGACAACTTGGTCATGCTGCACACGACAGAAAAAGGAGGAAGGGCCTACAAACATGCTCTGAATGAACTACCAGAAACCCTGGAAACATTCATGCTCCTAGCTCTGTTGGCTGCGATGACAGGAGGAATCTTTCTGTTCTTGATGTAAGGAAGAGGTATAGGGAAAATGTCCATGGGACTGATCTGCATAATGGCAGCCAGCGGCCTGCTATGGATGGCAGAAATCCAGCCCCATTGGATAGCGGCCTCAATAATACTGGAGTTTTTTCTCATGGTACTGCTTATTCCAGAACCAGAAAAGCAGAGAACTCCCCAGGACAACCAATTGACCTATGTCGTGATAGCCATCCTCACAATGGTTGCAACAATAGCAGCCAATGAAATGGGATTGTTGGAAAAAACAAAGAAAGATCTTGGGTTTGGCCATGTAGCAACTGAAAATACAATTCTGGACGTAGATCTACGTCCAGCATCAGCATGGACACTCTATGCAGTGGCCACAACAATTATCACACCAATGTTGAGACACACCATAGAAAACTCCTCAGCAAATGTGTCCCTGACAGCCATTGCCAACCAGGCAGCGGTCTTGATGGGTCTTGGAAAAGGATGGCCATTATCGAAAATGGACATAGGAGTTCCACTTCTCGCCTTGGGATGCTATTCACAAGTGAACCCAATAACTCTCACAGCAGCACTACTTTTGCTAGTGGCACATTATGCCATAATAGGTCCAGGACTGCAAGCAAAAGCCACTAGAGAAGCTCAGAAAAGGACAGCAGCTGGAATCATGAAGAATCCAACGGTGGATGGGATAACAGTAATAGACCTAGATCCAATACCCTATGATCCAAAATTTGAAAAGCAGTTAGGACAAGTAATGCTCCTGGTCCTTTGTGCAGCACAGCTACTGTTGATGAGAACTACATGGGCTTTGTGTGAAGCCTTAACCCTAGCCACAGGACCAATATCAACACTGTGGGAAGGAAATCCAGGGAAATTCTGGAACACAACGATAGCTGTGTCCATGGCTAACATTTTCAGAGGGAGTTATTTGGCCGGAGCTGGACTTGCTTTTTCTATCATGAAGAATGCAGGAAGCGCAAGGAGAGGAACTGGGACCATAGGAGAAACACTGGGAGAAAAATGGAAAAGACAACTAAACCCATTGGGCAGGAAAGAATTCGAAATATACAAGAAAAGTGGAATTCTAGAAGTGGACAGAACCGAAGCCAAAGAAGGCTTGAAAAGAGGAGAAACAACCCACCATGCCGTGTCGAGAGGCTCCGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCAAACCAGAAGGGAAAGTCGTAGACCTTGGTTGTGGAAGAGGAGGCTGGTCATATTACTGTGCGGGACTGAAGAATGTGACAGAAGTGAAAGGATACACAAAAGGAGGACCAGGACATGAAGAACCAATCCCTATGTCTACATATGGATGGAACCTAGTCAAGCTTCAGAGTGGAGTGGATGTGTTCTTCACTCCACCTGAGAAATGTGACACCCTGTTGTGTGACATTGGGGAATCATCACCAAATCCAACAGTAGAAGAAGGAAGAACATTAAGAGTTCTGAAGATGGTGGAACCATGGCTCAACAACAACACTCAATTTTGCATAAAAGTTCTCAACCCCTACATGCCAACAGTCATAGAAAAACTGGAAAAACTACAAAGGAAACATGGAGGAATCCTTGTGAGAAATCCACTCTCACGAAATTCCACCCATGAGATGTACTGGGTGTCCAATGCTTCAGGAAACATTGTGTCTTCAGTGAACATGATATCAAGAATGTTGCTGAACAGATTCACAATGAGACACAGGAAACCCACTTATGAGAAAGACGTGGACCTTGGAGCTGGAACACGAAATGTCGCAATTGAAACAGAAACACCAAACATGGATATCATTGGGAAAAGGATAGAGAAAATAAAAGAAGAGCATAAAACAACATGGCACTATGATCAGGACAATCCATACAAAACATGGGCTTACCATGGAAGCTATGAAGCCAAACCGACAGGATCAGCATCATCCATGGTGAATGGAGTGGTGAGACTGCTGACAAAACCCTGGGACGTGATTCCCATGGTGACACAGATGGCAATGACAGACACAACTCCCTTTGGACAACAGAGAGTTTTTAAAGAGAAAGTGGACACGAGAACACCAAAACCAAAACCAGGCACAAGAAAAGTTATGAAGATCACAGCCGAGTGGCTTTGGAGATTCCTTGGAAGGAAAAAAAAACCCAGAATGTGCACAAGAGAAGAGTTCACAAAAAAAGTTAGAACCAACGCAGCTATGGGCGCCGTGTTCACTGATGAGAACAAATGGAACTCAGCAAGTGAAGCTGTTGAAGACGAACGGTTTTGGGAACTGGTGGACAAAGAAAGGGATCTTCACCAAGAAGGAAAGTGTGAAACGTGTGTCTACAACATGATGGGAAAAAGAGAGAAGAAACTAGGAGAGTTTGGCAAAGCAAAAGGCAGCAGAGCAATATGGTACATGTGGCTGGGAGCACGCTTCCTAGAGTTTGAAGCCCTAGGTTTCTTGAATGAAGACCACTGGTTCTCCAGAGAAAATTCACTGAGTGGAGTGGAAGGAGAAGGACTGCACAAGCTGGGATACATCCTAAGAGACATAAACAAGAAAGAAGGAGGAGCAATGTATGCTGATGACACAGCTGGTTGGGACACAAGAATCACAGAAGATGACCTGCAGAATGAAGAAATGATCACAGACCAAATGGACCCTGAACATAAGAAATTGGCCAAGGCCATTTTCAAACTAACATACCAAAACAAGGTGGTGAGAGTCCAAAGACCAACACCAAAAGGCACGGTGATGGATATCATATCCAGGAGAGACCAAAGAGGCAGTGGACAGGTTGGAACTTATGGTCTGAACACTTTCACCAACATGGAAGCACAACTAATCAGACAAATGGAAGGTGAAGGAGTCTTTACACCAAAAGAATTCTAGACCCCACATCTGCTAGAAAAAAGAGTTCAAGAATGGTTGGAAAAACATGGAGTCGAAAGGTTAAAAAGAATGGCAATCAGTGGAGATGATTGTGTGGTGAAACCACTAGATGACAGGTTCGCCACAGCCCTAACAGCTTTGAATGACATGGGAAAGGTTAGGAAAGACATACCGCAATGGGAACCTTCAAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGCTCCCACCACTTTCATGAGCTGATCATGAAAGATGGTCGCACGCTAGTAGTTCCATGCAGAAACCAAGATGAACTGATAGGTAGAGCCAGAATCTCTCAGGGAGCTGGATGGAGCTTGAGAGAAACAGCCTGTCTGGGGAAGTCTTACGCCCAAATGTGGAGGCTGATGTACTTCCACAGAAGAGATCTGAGGCTGGCGGCCAATGCCATATGTTCAGCAGTTCCAGTACATTGGGTTCCAACAAGCAGAACAACCTGGTCGATCCATGCCCACCATCAATGGATGACAACAGAAGACATGTTTACAGTCTGGAACAGGGTGTGGATAGAGGACAACCCATGGATGGAAGACAAAACTCCAGTCTAATCTTGGGAAGACATACCATACCTAGGGAAAAGAGAAGACCAGTGGTGTGGATCCCTGATTGGCCTAACATCCAGGGCCACCTGGGCAAAGAACATTCAAACAGCCATAAACCAAGTCAGAAGCCTCATTGGGAATGAGGAGTATATAGATTACATGCCATCAATGAAAAGATTCAGGAATGAGGAGGAGAACGAAGGAGTTCTGTGGTAAACAGCAAAAGAAGTCAGGCATAAAAGAAGTCAGGCCACTAATGCCACGGCTTGAGCAAACCGTGCTGCCTGTAGCTCCACCAAAAAGGGGAGGTGTAAAAAAACCCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGTGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCATGACAGACAAAACGCAGCACAAGGGGGCCCAAAGCCAGGAGGAAGCTGTACTCTCGTTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAAAACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT", "2K": "TPQDNQLTYVVIAILTMVATIAA", "C": "NNQRKKAGKPPFNMLKRERNRVSTVQQLAKRFSIGLL*GQGPLKLVMAFIAFLRFLAIPPTAGILKRWGTFKKSKAIKVLRGFRKEIGSMLNILNRRKRTAIILMMLIPTVMA", "E": "MRCVGVGNRDFVEGVSGGTWVDVVLEHGSCVTTMAKNKPTLDFELMKTEAKQPATLRKFCIEAKITNTTTESRCPTQGEPNLVEEQDQKFVCKQTMVDRGWGNGCGLFGKGGIVTCAKFTCLKKIEGKVVQPENLEYTVVITVHTGDEHAVGNDTTKHGMTAKITPQASTAEAKLTDYGTLTLDCSPRTGLDFNEMVLLKMKNKAWLVHRQWFLDLPLPWTSGADT*EANWNQKEMLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQTSGGNLMFAGHLKCRLRMDKLKLKGMSYAMCTGKFKIEKEMAETQHGTIVIKVKYEGDGAPCKIPFEIKDVKKKNVIGRLITANPIVTEKDSPVNIEAEPPFGDSYIVIGVGERALKLNWFKKGSSIGKMFEATARGAKRMAILGDTAWDFGSVGGVFTSVGKAVHQVFGTVYGAMFSGVSWTMKILIGVLITWIGMNSRSTSLSMTCIAVGIVTLYLGVMVQA", "M": "FHLTTRDGEPHMIVSKHERGKSLLFKTADGINMCTLIAMDLGELCEDTITYKCPLLTETEPEDIDCWCNPTSTWVTYGTCTQTGEHRREKRSVALAPHVGMGLETRTETWMSSEGAWKQAQRVETWILRHPGFTIMAVFLAYTIGTTYIQRVVIFILLMLVAPSMT", "NS1": "DMGCVVNWKGKELKCGSGIFVTDNVHTWTEQYKFQPDSPTRLASAIPKAHEEGVCGIRSATRLENLMWKQITNELNHILWENEIKLTVVAGDIKGILEKGKRTLTPQPIELKYSWKTWGKAKILTAEVQNNTFLIDGPDTPECPNDQRAWNFLEVEDYGFGIFTTNIWLKLREEYTEVCDHRLMSAAIKDNRAVHADMGYWIESAKNETWKIEKASFIEVKTCLWPKSHTLWSNGVLESEMIIPKIFAGPISQHNYRPGYYTQTAGPWHLGKLEMDFDFCEGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYIGEDGCWYGMEIRPLNEKEENLVKSLVTA", "NS2A": "GHGKVDNFSIGLLCMALFMEEVLRTRVGRKHMILVVVVTFVTLITGNMTWRDLVRVLIMVGATMSDRMGGVTYLALMAAFKMRPIFAVGLFLRKLTSREIILMTIGMALVTSFQIPDAIVELTDGIALGIMVLKMVTHFEKYQLGATILSLTCIKTTMTLHNAWKTITIILAVVSLFPLCLTSSLQKQTDWIPITLTIIGVKPLPMFLITLTKTSKKR", "NS2B": "SWPLNEGIMAVGMVSILASSLLKNDVPMAGPLVAGGLLIACYVITGSSADLSLEKAADVKWEEEAEISGASPIILVTVEEDGTMSIKDEEEENTLTILIKTALLVVSGLFPLSIPVTMAVWYMWQMKKQR", "NS3": "SGVLWDVPSPPAVEKAELEDGVYRIKQRGIFGKSQVGVGVYKEGVFHTMWHVTRGAVLMHKGKRLEPSWADVKKDLISYGGGWRLEGKWKKGEEVQVLAVEPGKNPKNVQTKPGLFKTTTGEIGAVALDFKPGTSGSPIINKKGKVVGLYGNGVVTKSGAYVSAIAQTEKIEEPNPEIEDDIFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRSLRTLILAPTRVVAAEMEEALRGLPISYQTPAMKAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAAIFMTATPPGTTDPFPQSNAPIKDEEREIPERSWNSGYEWITDFQGKTVWFVPSIKAGNDIANCLRKNGKRVIQLSRKTFDTEYPKTKINDWDFVVTTDISEMGANFKAERVIDPRRCLKPVILTDGPERVILAGPMPVTLASAAQRRGRIGRNPKKENDQYIYMGEPLKNDEDHAHWTEAKMLLDNINTPEGIIPTLFEPEREKTEAIDGEYRLRGEARKTFVELMRRGDLPVWLAYKVASEGIKYTDRRWCFDGERNNQILEENMEVEIWTKEGERKKLRPRWLDARTYSDPLALKEFKEFAAGRK", "NS4A": "SITLDLITEIGRLPTYLTHRARNALDNLVMLHTTEKGGRAYKHALNELPETLETFMLLALLAAMTGGIFLFLM*GRGIGKMSMGLICIMAASGLLWMAEIQPHWIAASIILEFFLMVLLIPEPEKQR", "NS4B": "NEMGLLEKTKKDLGFGHVATENTILDVDLRPASAWTLYAVATTIITPMLRHTIENSSANVSLTAIANQAAVLMGLGKGWPLSKMDIGVPLLALGCYSQVNPITLTAALLLLVAHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLDPIPYDPKFEKQLGQVMLLVLCAAQLLLMRTTWALCEALTLATGPISTLWEGNPGKFWNTTIAVSMANIFRGSYLAGAGLAFSIMKNAGSARR", "NS5": "GTGTIGETLGEKWKRQLNPLGRKEFEIYKKSGILEVDRTEAKEGLKRGETTHHAVSRGSAKLRWFVERNMVKPEGKVVDLGCGRGGWSYYCAGLKNVTEVKGYTKGGPGHEEPIPMSTYGWNLVKLQSGVDVFFTPPEKCDTLLCDIGESSPNPTVEEGRTLRVLKMVEPWLNNNTQFCIKVLNPYMPTVIEKLEKLQRKHGGILVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLLNRFTMRHRKPTYEKDVDLGAGTRNVAIETETPNMDIIGKRIEKIKEEHKTTWHYDQDNPYKTWAYHGSYEAKPTGSASSMVNGVVRLLTKPWDVIPMVTQMAMTDTTPFGQQRVFKEKVDTRTPKPKPGTRKVMKITAEWLWRFLGRKKKPRMCTREEFTKKVRTNAAMGAVFTDENKWNSASEAVEDERFWELVDKERDLHQEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWFSRENSLSGVEGEGLHKLGYILRDINKKEGGAMYADDTAGWDTRITEDDLQNEEMITDQMDPEHKKLAKAIFKLTYQNKVVRVQRPTPKGTVMDIISRRDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGVFTPKEF*TPHLLEKRVQEWLEKHGVERLKRMAISGDDCVVKPLDDRFATALTALNDMGKVRKDIPQWEPSKGWNDWQQVPFCSHHFHELIMKDGRTLVVPCRNQDELIGRARISQGAGWSLRETACLGKSYAQMWRLMYFHRRDLRLAANAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMFTVWNRVWIEDNPWMEDKTPV*SWEDIPYLGKREDQWCGSLIGLTSRATWAKNIQTAINQVRSLIGNEEYIDYMPSMKRFRNEEENEGVL", "pr": "FHLTTRDGEPHMIVSKHERGKSLLFKTADGINMCTLIAMDLGELCEDTITYKCPLLTETEPEDIDCWCNPTSTWVTYGTCTQTGEHRREKR"}} \ No newline at end of file diff --git a/nextclade/datasets/denv1/genome_annotation.gff3 b/nextclade/datasets/denv1/genome_annotation.gff3 index 14201ebb..aa3a8428 100644 --- a/nextclade/datasets/denv1/genome_annotation.gff3 +++ b/nextclade/datasets/denv1/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_001477.1 1 10735 -NC_001477.1 feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; -NC_001477.1 feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; -NC_001477.1 feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; -NC_001477.1 feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; -NC_001477.1 feature gene 2420 3475 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_001477.1 feature gene 3476 4129 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_001477.1 feature gene 4130 4519 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_001477.1 feature gene 4520 6376 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_001477.1 feature gene 6377 6757 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_001477.1 feature gene 6758 6826 . + . codon_start=1;gene=2K;gene_name=2K; -NC_001477.1 feature gene 6827 7573 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_001477.1 feature gene 7574 10270 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome 1 10735 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 2420 3475 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 3476 4129 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 4130 4519 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 4520 6376 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 6377 6757 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 6758 6826 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 6827 7573 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 7574 10270 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/datasets/denv1/pathogen.json b/nextclade/datasets/denv1/pathogen.json index 5ebe4c90..52d9ee02 100644 --- a/nextclade/datasets/denv1/pathogen.json +++ b/nextclade/datasets/denv1/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/datasets/denv1/reference.fasta b/nextclade/datasets/denv1/reference.fasta index 3a18135a..061492e4 100644 --- a/nextclade/datasets/denv1/reference.fasta +++ b/nextclade/datasets/denv1/reference.fasta @@ -1,180 +1,2 @@ ->NC_001477.1 Dengue virus 1, complete genome -AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGAATCGGAAGCTTGCTTAACGTAG -TTCTAACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGG -TCGACCGTCTTTCAATATGCTGAAACGCGCGAGAAACCGCGTGTCAACTGTTTCACAGTT -GGCGAAGAGATTCTCAAAAGGATTGCTTTCAGGCCAAGGACCCATGAAATTGGTGATGGC -TTTTATAGCATTCCTAAGATTTCTAGCCATACCTCCAACAGCAGGAATTTTGGCTAGATG -GGGCTCATTCAAGAAGAATGGAGCGATCAAAGTGTTACGGGGTTTCAAGAAAGAAATCTC -AAACATGTTGAACATAATGAACAGGAGGAAAAGATCTGTGACCATGCTCCTCATGCTGCT -GCCCACAGCCCTGGCGTTCCATCTGACCACCCGAGGGGGAGAGCCGCACATGATAGTTAG -CAAGCAGGAAAGAGGAAAATCACTTTTGTTTAAGACCTCTGCAGGTGTCAACATGTGCAC -CCTTATTGCAATGGATTTGGGAGAGTTATGTGAGGACACAATGACCTACAAATGCCCCCG -GATCACTGAGACGGAACCAGATGACGTTGACTGTTGGTGCAATGCCACGGAGACATGGGT -GACCTATGGAACATGTTCTCAAACTGGTGAACACCGACGAGACAAACGTTCCGTCGCACT -GGCACCACACGTAGGGCTTGGTCTAGAAACAAGAACCGAAACGTGGATGTCCTCTGAAGG -CGCTTGGAAACAAATACAAAAAGTGGAGACCTGGGCTCTGAGACACCCAGGATTCACGGT -GATAGCCCTTTTTCTAGCACATGCCATAGGAACATCCATCACCCAGAAAGGGATCATTTT -TATTTTGCTGATGCTGGTAACTCCATCCATGGCCATGCGGTGCGTGGGAATAGGCAACAG -AGACTTCGTGGAAGGACTGTCAGGAGCTACGTGGGTGGATGTGGTACTGGAGCATGGAAG -TTGCGTCACTACCATGGCAAAAGACAAACCAACACTGGACATTGAACTCTTGAAGACGGA -GGTCACAAACCCTGCCGTCCTGCGCAAACTGTGCATTGAAGCTAAAATATCAAACACCAC -CACCGATTCGAGATGTCCAACACAAGGAGAAGCCACGCTGGTGGAAGAACAGGACACGAA -CTTTGTGTGTCGACGAACGTTCGTGGACAGAGGCTGGGGCAATGGTTGTGGGCTATTCGG -AAAAGGTAGCTTAATAACGTGTGCTAAGTTTAAGTGTGTGACAAAACTGGAAGGAAAGAT -AGTCCAATATGAAAACTTAAAATATTCAGTGATAGTCACCGTACACACTGGAGACCAGCA -CCAAGTTGGAAATGAGACCACAGAACATGGAACAACTGCAACCATAACACCTCAAGCTCC -CACGTCGGAAATACAGCTGACAGACTACGGAGCTCTAACATTGGATTGTTCACCTAGAAC -AGGGCTAGACTTTAATGAGATGGTGTTGTTGACAATGAAAAAAAAATCATGGCTCGTCCA -CAAACAATGGTTTCTAGACTTACCACTGCCTTGGACCTCGGGGGCTTCAACATCCCAAGA -GACTTGGAATAGACAAGACTTGCTGGTCACATTTAAGACAGCTCATGCAAAAAAGCAGGA -AGTAGTCGTACTAGGATCACAAGAAGGAGCAATGCACACTGCGTTGACTGGAGCGACAGA -AATCCAAACGTCTGGAACGACAACAATTTTTGCAGGACACCTGAAATGCAGATTAAAAAT -GGATAAACTGATTTTAAAAGGGATGTCATATGTAATGTGCACAGGGTCATTCAAGTTAGA -GAAGGAAGTGGCTGAGACCCAGCATGGAACTGTTCTAGTGCAGGTTAAATACGAAGGAAC -AGATGCACCATGCAAGATCCCCTTCTCGTCCCAAGATGAGAAGGGAGTAACCCAGAATGG -GAGATTGATAACAGCCAACCCCATAGTCACTGACAAAGAAAAACCAGTCAACATTGAAGC -GGAGCCACCTTTTGGTGAGAGCTACATTGTGGTAGGAGCAGGTGAAAAAGCTTTGAAACT -AAGCTGGTTCAAGAAGGGAAGCAGTATAGGGAAAATGTTTGAAGCAACTGCCCGTGGAGC -ACGAAGGATGGCCATCCTGGGAGACACTGCATGGGACTTCGGTTCTATAGGAGGGGTGTT -CACGTCTGTGGGAAAACTGATACACCAGATTTTTGGGACTGCGTATGGAGTTTTGTTCAG -CGGTGTTTCTTGGACCATGAAGATAGGAATAGGGATTCTGCTGACATGGCTAGGATTAAA -CTCAAGGAGCACGTCCCTTTCAATGACGTGTATCGCAGTTGGCATGGTCACACTGTACCT -AGGAGTCATGGTTCAGGCGGACTCGGGATGTGTAATCAACTGGAAAGGCAGAGAACTCAA -ATGTGGAAGCGGCATTTTTGTCACCAATGAAGTCCACACCTGGACAGAGCAATATAAATT -CCAGGCCGACTCCCCTAAGAGACTATCAGCGGCCATTGGGAAGGCATGGGAGGAGGGTGT -GTGTGGAATTCGATCAGCCACTCGTCTCGAGAACATCATGTGGAAGCAAATATCAAATGA -ATTAAACCACATCTTACTTGAAAATGACATGAAATTTACAGTGGTCGTAGGAGACGTTAG -TGGAATCTTGGCCCAAGGAAAGAAAATGATTAGGCCACAACCCATGGAACACAAATACTC -GTGGAAAAGCTGGGGAAAAGCCAAAATCATAGGAGCAGATGTACAGAATACCACCTTCAT -CATCGACGGCCCAAACACCCCAGAATGCCCTGATAACCAAAGAGCATGGAACATTTGGGA -AGTTGAAGACTATGGATTTGGAATTTTCACGACAAACATATGGTTGAAATTGCGTGACTC -CTACACTCAAGTGTGTGACCACCGGCTAATGTCAGCTGCCATCAAGGATAGCAAAGCAGT -CCATGCTGACATGGGGTACTGGATAGAAAGTGAAAAGAACGAGACTTGGAAGTTGGCAAG -AGCCTCCTTCATAGAAGTTAAGACATGCATCTGGCCAAAATCCCACACTCTATGGAGCAA -TGGAGTCCTGGAAAGTGAGATGATAATCCCAAAGATATATGGAGGACCAATATCTCAGCA -CAACTACAGACCAGGATATTTCACACAAACAGCAGGGCCGTGGCACTTGGGCAAGTTAGA -ACTAGATTTTGATTTATGTGAAGGTACCACTGTTGTTGTGGATGAACATTGTGGAAATCG -AGGACCATCTCTTAGAACCACAACAGTCACAGGAAAGACAATCCATGAATGGTGCTGTAG -ATCTTGCACGTTACCCCCCCTACGTTTCAAAGGAGAAGACGGGTGCTGGTACGGCATGGA -AATCAGACCAGTCAAGGAGAAGGAAGAGAACCTAGTTAAGTCAATGGTCTCTGCAGGGTC -AGGAGAAGTGGACAGTTTTTCACTAGGACTGCTATGCATATCAATAATGATCGAAGAGGT -AATGAGATCCAGATGGAGCAGAAAAATGCTGATGACTGGAACATTGGCTGTGTTCCTCCT -TCTCACAATGGGACAATTGACATGGAATGATCTGATCAGGCTATGTATCATGGTTGGAGC -CAACGCTTCAGACAAGATGGGGATGGGAACAACGTACCTAGCTTTGATGGCCACTTTCAG -AATGAGACCAATGTTCGCAGTCGGGCTACTGTTTCGCAGATTAACATCTAGAGAAGTTCT -TCTTCTTACAGTTGGATTGAGTCTGGTGGCATCTGTAGAACTACCAAATTCCTTAGAGGA -GCTAGGGGATGGACTTGCAATGGGCATCATGATGTTGAAATTACTGACTGATTTTCAGTC -ACATCAGCTATGGGCTACCTTGCTGTCTTTAACATTTGTCAAAACAACTTTTTCATTGCA -CTATGCATGGAAGACAATGGCTATGATACTGTCAATTGTATCTCTCTTCCCTTTATGCCT -GTCCACGACTTCTCAAAAAACAACATGGCTTCCGGTGTTGCTGGGATCTCTTGGATGCAA -ACCACTAACCATGTTTCTTATAACAGAAAACAAAATCTGGGGAAGGAAAAGCTGGCCTCT -CAATGAAGGAATTATGGCTGTTGGAATAGTTAGCATTCTTCTAAGTTCACTTCTCAAGAA -TGATGTGCCACTAGCTGGCCCACTAATAGCTGGAGGCATGCTAATAGCATGTTATGTCAT -ATCTGGAAGCTCGGCCGATTTATCACTGGAGAAAGCGGCTGAGGTCTCCTGGGAAGAAGA -AGCAGAACACTCTGGTGCCTCACACAACATACTAGTGGAGGTCCAAGATGATGGAACCAT -GAAGATAAAGGATGAAGAGAGAGATGACACACTCACCATTCTCCTCAAAGCAACTCTGCT -AGCAATCTCAGGGGTATACCCAATGTCAATACCGGCGACCCTCTTTGTGTGGTATTTTTG -GCAGAAAAAGAAACAGAGATCAGGAGTGCTATGGGACACACCCAGCCCTCCAGAAGTGGA -AAGAGCAGTCCTTGATGATGGCATTTATAGAATTCTCCAAAGAGGATTGTTGGGCAGGTC -TCAAGTAGGAGTAGGAGTTTTTCAAGAAGGCGTGTTCCACACAATGTGGCACGTCACCAG -GGGAGCTGTCCTCATGTACCAAGGGAAGAGACTGGAACCAAGTTGGGCCAGTGTCAAAAA -AGACTTGATCTCATATGGAGGAGGTTGGAGGTTTCAAGGATCCTGGAACGCGGGAGAAGA -AGTGCAGGTGATTGCTGTTGAACCGGGGAAGAACCCCAAAAATGTACAGACAGCGCCGGG -TACCTTCAAGACCCCTGAAGGCGAAGTTGGAGCCATAGCTCTAGACTTTAAACCCGGCAC -ATCTGGATCTCCTATCGTGAACAGAGAGGGAAAAATAGTAGGTCTTTATGGAAATGGAGT -GGTGACAACAAGTGGTACCTACGTCAGTGCCATAGCTCAAGCTAAAGCATCACAAGAAGG -GCCTCTACCAGAGATTGAGGACGAGGTGTTTAGGAAAAGAAACTTAACAATAATGGACCT -ACATCCAGGATCGGGAAAAACAAGAAGATACCTTCCAGCCATAGTCCGTGAGGCCATAAA -AAGAAAGCTGCGCACGCTAGTCTTAGCTCCCACAAGAGTTGTCGCTTCTGAAATGGCAGA -GGCGCTCAAGGGAATGCCAATAAGGTATCAGACAACAGCAGTGAAGAGTGAACACACGGG -AAAGGAGATAGTTGACCTTATGTGTCACGCCACTTTCACTATGCGTCTCCTGTCTCCTGT -GAGAGTTCCCAATTATAATATGATTATCATGGATGAAGCACATTTTACCGATCCAGCCAG -CATAGCAGCCAGAGGGTATATCTCAACCCGAGTGGGTATGGGTGAAGCAGCTGCGATTTT -CATGACAGCCACTCCCCCCGGATCGGTGGAGGCCTTTCCACAGAGCAATGCAGTTATCCA -AGATGAGGAAAGAGACATTCCTGAAAGATCATGGAACTCAGGCTATGACTGGATCACTGA -TTTCCCAGGTAAAACAGTCTGGTTTGTTCCAAGCATCAAATCAGGAAATGACATTGCCAA -CTGTTTAAGAAAGAATGGGAAACGGGTGGTCCAATTGAGCAGAAAAACTTTTGACACTGA -GTACCAGAAAACAAAAAATAACGACTGGGACTATGTTGTCACAACAGACATATCCGAAAT -GGGAGCAAACTTCCGAGCCGACAGGGTAATAGACCCGAGGCGGTGCCTGAAACCGGTAAT -ACTAAAAGATGGCCCAGAGCGTGTCATTCTAGCCGGACCGATGCCAGTGACTGTGGCTAG -CGCCGCCCAGAGGAGAGGAAGAATTGGAAGGAACCAAAATAAGGAAGGCGATCAGTATAT -TTACATGGGACAGCCTCTAAACAATGATGAGGACCACGCCCATTGGACAGAAGCAAAAAT -GCTCCTTGACAACATAAACACACCAGAAGGGATTATCCCAGCCCTCTTTGAGCCGGAGAG -AGAAAAGAGTGCAGCAATAGACGGGGAATACAGACTACGGGGTGAAGCGAGGAAAACGTT -CGTGGAGCTCATGAGAAGAGGAGATCTACCTGTCTGGCTATCCTACAAAGTTGCCTCAGA -AGGCTTCCAGTACTCCGACAGAAGGTGGTGCTTTGATGGGGAAAGGAACAACCAGGTGTT -GGAGGAGAACATGGACGTGGAGATCTGGACAAAAGAAGGAGAAAGAAAGAAACTACGACC -CCGCTGGCTGGATGCCAGAACATACTCTGACCCACTGGCTCTGCGCGAATTCAAAGAGTT -CGCAGCAGGAAGAAGAAGCGTCTCAGGTGACCTAATATTAGAAATAGGGAAACTTCCACA -ACATTTAACGCAAAGGGCCCAGAACGCCTTGGACAATCTGGTTATGTTGCACAACTCTGA -ACAAGGAGGAAAAGCCTATAGACACGCCATGGAAGAACTACCAGACACCATAGAAACGTT -AATGCTCCTAGCTTTGATAGCTGTGCTGACTGGTGGAGTGACGTTGTTCTTCCTATCAGG -AAGGGGTCTAGGAAAAACATCCATTGGCCTACTCTGCGTGATTGCCTCAAGTGCACTGTT -ATGGATGGCCAGTGTGGAACCCCATTGGATAGCGGCCTCTATCATACTGGAGTTCTTTCT -GATGGTGTTGCTTATTCCAGAGCCGGACAGACAGCGCACTCCACAAGACAACCAGCTAGC -ATACGTGGTGATAGGTCTGTTATTCATGATATTGACAGTGGCAGCCAATGAGATGGGATT -ACTGGAAACCACAAAGAAGGACCTGGGGATTGGTCATGCAGCTGCTGAAAACCACCATCA -TGCTGCAATGCTGGACGTAGACCTACATCCAGCTTCAGCCTGGACTCTCTATGCAGTGGC -CACAACAATTATCACTCCCATGATGAGACACACAATTGAAAACACAACGGCAAATATTTC -CCTGACAGCTATTGCAAACCAGGCAGCTATATTGATGGGACTTGACAAGGGATGGCCAAT -ATCAAAGATGGACATAGGAGTTCCACTTCTCGCCTTGGGGTGCTATTCTCAGGTGAACCC -GCTGACGCTGACAGCGGCGGTATTGATGCTAGTGGCTCATTATGCCATAATTGGACCCGG -ACTGCAAGCAAAAGCTACTAGAGAAGCTCAAAAAAGGACAGCAGCCGGAATAATGAAAAA -CCCAACTGTCGACGGGATCGTTGCAATAGATTTGGACCCTGTGGTTTACGATGCAAAATT -TGAAAAACAGCTAGGCCAAATAATGTTGTTGATACTTTGCACATCACAGATCCTCCTGAT -GCGGACCACATGGGCCTTGTGTGAATCCATCACACTAGCCACTGGACCTCTGACTACGCT -TTGGGAGGGATCTCCAGGAAAATTCTGGAACACCACGATAGCGGTGTCCATGGCAAACAT -TTTTAGGGGAAGTTATCTAGCAGGAGCAGGTCTGGCCTTTTCATTAATGAAATCTCTAGG -AGGAGGTAGGAGAGGCACGGGAGCCCAAGGGGAAACACTGGGAGAAAAATGGAAAAGACA -GCTAAACCAATTGAGCAAGTCAGAATTCAACACTTACAAAAGGAGTGGGATTATAGAGGT -GGATAGATCTGAAGCCAAAGAGGGGTTAAAAAGAGGAGAAACGACTAAACACGCAGTGTC -GAGAGGAACGGCCAAACTGAGGTGGTTTGTGGAGAGGAACCTTGTGAAACCAGAAGGGAA -AGTCATAGACCTCGGTTGTGGAAGAGGTGGCTGGTCATATTATTGCGCTGGGCTGAAGAA -AGTCACAGAAGTGAAAGGATACACGAAAGGAGGACCTGGACATGAGGAACCAATCCCAAT -GGCAACCTATGGATGGAACCTAGTAAAGCTATACTCCGGGAAAGATGTATTCTTTACACC -ACCTGAGAAATGTGACACCCTCTTGTGTGATATTGGTGAGTCCTCTCCGAACCCAACTAT -AGAAGAAGGAAGAACGTTACGTGTTCTAAAGATGGTGGAACCATGGCTCAGAGGAAACCA -ATTTTGCATAAAAATTCTAAATCCCTATATGCCGAGTGTGGTAGAAACTTTGGAGCAAAT -GCAAAGAAAACATGGAGGAATGCTAGTGCGAAATCCACTCTCAAGAAACTCCACTCATGA -AATGTACTGGGTTTCATGTGGAACAGGAAACATTGTGTCAGCAGTAAACATGACATCTAG -AATGCTGCTAAATCGATTCACAATGGCTCACAGGAAGCCAACATATGAAAGAGACGTGGA -CTTAGGCGCTGGAACAAGACATGTGGCAGTAGAACCAGAGGTGGCCAACCTAGATATCAT -TGGCCAGAGGATAGAGAATATAAAAAATGAACACAAATCAACATGGCATTATGATGAGGA -CAATCCATACAAAACATGGGCCTATCATGGATCATATGAGGTCAAGCCATCAGGATCAGC -CTCATCCATGGTCAATGGTGTGGTGAGACTGCTAACCAAACCATGGGATGTCATTCCCAT -GGTCACACAAATAGCCATGACTGACACCACACCCTTTGGACAACAGAGGGTGTTTAAAGA -GAAAGTTGACACGCGTACACCAAAAGCGAAACGAGGCACAGCACAAATTATGGAGGTGAC -AGCCAGGTGGTTATGGGGTTTTCTCTCTAGAAACAAAAAACCCAGAATCTGCACAAGAGA -GGAGTTCACAAGAAAAGTCAGGTCAAACGCAGCTATTGGAGCAGTGTTCGTTGATGAAAA -TCAATGGAACTCAGCAAAAGAGGCAGTGGAAGATGAACGGTTCTGGGACCTTGTGCACAG -AGAGAGGGAGCTTCATAAACAAGGAAAATGTGCCACGTGTGTCTACAACATGATGGGAAA -GAGAGAGAAAAAATTAGGAGAGTTCGGAAAGGCAAAAGGAAGTCGCGCAATATGGTACAT -GTGGTTGGGAGCGCGCTTTTTAGAGTTTGAAGCCCTTGGTTTCATGAATGAAGATCACTG -GTTCAGCAGAGAGAATTCACTCAGTGGAGTGGAAGGAGAAGGACTCCACAAACTTGGATA -CATACTCAGAGACATATCAAAGATTCCAGGGGGAAATATGTATGCAGATGACACAGCCGG -ATGGGACACAAGAATAACAGAGGATGATCTTCAGAATGAGGCCAAAATCACTGACATCAT -GGAACCTGAACATGCCCTATTGGCCACGTCAATCTTTAAGCTAACCTACCAAAACAAGGT -AGTAAGGGTGCAGAGACCAGCGAAAAATGGAACCGTGATGGATGTCATATCCAGACGTGA -CCAGAGAGGAAGTGGACAGGTTGGAACCTATGGCTTAAACACCTTCACCAACATGGAGGC -CCAACTAATAAGACAAATGGAGTCTGAGGGAATCTTTTCACCCAGCGAATTGGAAACCCC -AAATCTAGCCGAAAGAGTCCTCGACTGGTTGAAAAAACATGGCACCGAGAGGCTGAAAAG -AATGGCAATCAGTGGAGATGACTGTGTGGTGAAACCAATCGATGACAGATTTGCAACAGC -CTTAACAGCTTTGAATGACATGGGAAAGGTAAGAAAAGACATACCGCAATGGGAACCTTC -AAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGTTCACACCATTTCCACCAGCTGAT -TATGAAGGATGGGAGGGAGATAGTGGTGCCATGCCGCAACCAAGATGAACTTGTAGGTAG -GGCCAGAGTATCACAAGGCGCCGGATGGAGCTTGAGAGAAACTGCATGCCTAGGCAAGTC -ATATGCACAAATGTGGCAGCTGATGTACTTCCACAGGAGAGACTTGAGATTAGCGGCTAA -TGCTATCTGTTCAGCCGTTCCAGTTGATTGGGTCCCAACCAGCCGCACCACCTGGTCGAT -CCATGCCCACCATCAATGGATGACAACAGAAGACATGTTGTCAGTGTGGAATAGGGTTTG -GATAGAGGAAAACCCATGGATGGAGGACAAGACTCATGTGTCCAGTTGGGAAGACGTTCC -ATACCTAGGAAAAAGGGAAGATCAATGGTGTGGTTCCCTAATAGGCTTAACAGCACGAGC -CACCTGGGCCACCAACATACAAGTGGCCATAAACCAAGTGAGAAGGCTCATTGGGAATGA -GAATTATCTAGACTTCATGACATCAATGAAGAGATTCAAAAACGAGAGTGATCCCGAAGG -GGCACTCTGGTAAGCCAACTCATTCACAAAATAAAGGAAAATAAAAAATCAAACAAGGCA -AGAAGTCAGGCCGGATTAAGCCATAGCACGGTAAGAGCTATGCTGCCTGTGAGCCCCGTC -CAAGGACGTAAAATGAAGTCAGGCCGAAAGCCACGGTTCGAGCAAGCCGTGCTGCCTGTA -GCTCCATCGTGGGGATGTAAAAACCCGGGAGGCTGCAAACCATGGAAGCTGTACGCATGG -GGTAGCAGACTAGTGGTTAGAGGAGACCCCTCCCAAGACACAACGCAGCAGCGGGGCCCA -ACACCAGGGGAAGCTGTACCCTGGTGGTAAGGACTAGAGGTTAGAGGAGACCCCCCGCAC -AACAACAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCTACAGCATC -ATTCCAGGCACAGAACGCCAAAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome +AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGAATCGGAAGCTTGCTTAACGTAGTTCTAACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGTCGACCGTCTTTCAATATGCTGAAACGCGCGAGAAACCGCGTGTCAACTGTTTCACAGTTGGCGAAGAGATTCTCAAAAGGATTGCTCTCAGGCCAAGGACCCATGAAATTGGTGATGGCTTTCATAGCATTCCTAAGATTTCTAGCCATACCCCCAACAGCAGGAATTTTGGCTAGATGGGGCTCATTCAAGAAGAATGGAGCGATTAAAGTGTTACGGGGTTTCAAGAAAGAAATCTCAAACATGTTGAACATAATGAACAGGAGGAAAAGATCCGTGACCATGCTCCTTATGCTGCTGCCCACAGCCCTGGCGTTCCATCTGACCACACGAGGGGGAGAGCCGCACATGATAGTTAGCAAGCAGGAAAGAGGAAAGTCACTTTTGTTTAAGACCTCTGCAGGTGTCAACATGTGCACCCTTATTGCGATGGATTTGGGAGAGTTATGTGAGGACACAATGACCTACAAATGCCCCCGGATCACTGAGGCGGAACCAGATGACGTTGACTGTTGGTGCAATGCCACGGACACATGGGTGACCTATGGAACGTGTTCTCAAACTGGCGAACACCGACGAGACAAACGTTCCGTCGCACTGGCCCCACACGTGGGGCTTGGTCTAGAAACAAGAACCGAAACGTGGATGTCCTCTGAAGGCGCTTGGAAACAAATACAAAAAGTGGAGACTTGGGCTCTGAGACACCCAGGATTCACGGTGATAGCCCTTTTTCTAGCACATGCCATAGGAACATCCATCACCCAGAAAGGGATTATTTTCATTTTGCTGATGCTGGTAACACCATCCATGGCCATGCGATGCGTGGGAATAGGCAACAGAGACTTCGTGGAAGGACTGTCAGGAGCAACGTGGGTGGATGTGGTACTGGAGCATGGAAGTTGCGTCACCACCATGGCAAAAAATAAACCAACATTGGACATTGAACTCTTGAAGACGGAGGTCACAAACCCTGCCGTCCTGCGCAAACTGTGCATTGAAGCTAAAATATCAAACACCACCACCGATTCAAGATGTCCAACACAAGGAGAAGCCACACTGGTGGAAGAACAAGACGCGAACTTTGTGTGTCGACGAACGTTCGTGGACAGAGGCTGGGGCAATGGCTGTGGGCTATTCGGAAAAGGTAGCCTAATAACGTGTGCTAAGTTCAAGTGTGTGACAAAACTAGAAGGAAAGATAGTTCAATATGAAAACTTAAAATATTCAGTGATAGTCACCGTCCACACTGGAGACCAGCACCAGGTGGGAAATGAGACCACAGAACATGGAACAACTGCAACCATAACACCTCAAGCTCCTACGTCGGAAATACAGCTGACCGACTACGGAGCCCTTACATTGGATTGCTCACCTAGAACAGGGCTAGACTTTAATGAGATGGTGTTGTTGACAATGAAAGAAAAATCATGGCTTGTCCACAAACAATGGTTTCTAGACTTACCACTGCCTTGGACCTCGGGGGCTTCAACATCCCAAGAGACTTGGAACAGACAAGATTTGCTGGTCACATTTAAGACAGCTCATGCAAAGAAGCAGGAAGTAGTCGTACTAGGATCACAAGAAGGAGCAATGCACACTGCGTTGACTGGAGCGACAGAAATCCAAACGTCAGGAACGACAACAATTTTTGCAGGACACCTGAAATGCAGACTAAAAATGGACAAACTGACTTTAAAAGGGATGTCATATGTGATGTGCACAGGCTCATTCAAGTTAGAGAAAGAAGTGGCTGAGACCCAGCATGGAACTGTTCTAGTGCAGGTTAAATACGAAGGAACAGATGCACCATGCAAGATCCCCTTTTCGACCCAAGATGAGAAAGGAGTAACCCAGAATGGGAGATTGATAACAGCCAACCCCATAGTCACTGACAAAGAAAAACCAGTCAACATTGAGGCAGAACCACCTTTTGGTGAGAGCTACATCGTGGTAGGAGCAGGTGAAAAAGCTTTGAAACTAAGCTGGTTCAAGAAAGGAAGCAGCATAGGGAAAATGTTTGAAGCAACTGCCCGAGGAGCACGAAGGATGGCCATCCTGGGAGACACCGCATGGGACTTCGGTTCTATAGGAGGAGTGTTCACGTCTGTGGGAAAACTGGTACACCAGGTTTTTGGAACTGCATATGGAGTTTTGTTCAGCGGTGTTTCTTGGACCATGAAAATAGGAATAGGGATTCTGCTGACATGGCTAGGATTAAATTCAAGGAGCACGTCCCTTTCGATGACGTGCATTGCAGTTGGCATGGTCACACTGTACCTAGGAGTCATGGTTCAGGCGGACTCGGGATGTGTAATCAACTGGAAAGGCAGAGAACTCAAATGTGGAAGTGGCATTTTTGTCACTAATGAAGTTCACACTTGGACAGAGCAATACAAATTCCAGGCTGACTCCCCAAAGAGACTATCAGCAGCCATTGGGAAGGCATGGGAGGAGGGTGTGTGTGGAATTCGATCAGCCACTCGTCTCGAGAACATCATGTGGAAGCAAATATCAAATGAATTGAACCACATCCTACTTGAAAATGACATGAAATTCACAGTGGTCGTAGGAGATGTTAGTGGAATCTTGGCCCAAGGAAAAAAAATGATTAGGCCACAACCCATGGAACACAAATACTCGTGGAAAAGCTGGGGAAAAGCCAAAATCATAGGAGCAGATGTACAGAACACCACCTTCATCATCGACGGCCCAAACACCCCAGAATGCCCTGATGACCAAAGAGCATGGAACATTTGGGAAGTTGAGGACTATGGATTTGGAATTTTCACGACAAACATATGGTTGAAATTGCGTGACTCCTACACCCAAGTGTGTGACCACCGGCTAATGTCAGCTGCCATCAAGGACAGCAAGGCAGTCCATGCTGACATGGGGTACTGGATAGAAAGTGAAAAGAACGAGACCTGGAAGCTGGCGAGAGCCTCCTTCATAGAAGTTAAGACATGCATCTGGCCAAAATCCCACACTCTATGGAGCAATGGAGTTCTGGAAAGTGAAATGATAATCCCAAAGATATATGGAGGACCAATATCTCAGCACAACTACAGACCAGGATATTTCACACAAACAGCAGGGCCGTGGCACCTAGGCAAGTTGGAACTAGATTTTGATTTGTGTGAAGGTACCACAGTTGTTGTGGATGAACATTGTGGAAATCGAGGACCATCTCTTAGAACCACAACAGTCACAGGAAAGATAATCCATGAATGGTGCTGCAGATCTTGTACGCTACCCCCCTTACGTTTCAAAGGAGAAGACGGGTGTTGGTACGGCATGGAAATCAGACCAGTCAAGGAGAAGGAAGAGAACCTAGTCAAGTCAATGGTCTCTGCAGGGTCAGGAGAAGTGGACAGCTTTTCACTAGGACTGCTATGCATATCAATAATGATTGAAGAGGTGATGAGATCCAGATGGAGTAGAAAAATGCTGATGACTGGAACACTGGCTGTGTTCCTCCTTCTTATAATGGGACAATTGACATGGAATGATCTGATCAGGTTATGCATCATGGTTGGAGCCAATGCTTCAGACAGGATGGGGATGGGAACAACGTACCTAGCTTTGATGGCCACTTTCAAAATGAGACCAATGTTCGCTGTCGGGCTATTATTTCGCAGACTAACATCTAGAGAAGTTCTTCTTCTTACAATTGGATTGAGCCTGGTGGCATCCGTGGAGCTACCAAATTCCTTAGAGGAGCTGGGGGATGGACTTGCAATGGGCATCATGATGTTAAAATTACTGACTGATTTTCAGTCACACCAGCTATGGGCTACCTTGCTGTCCTTGACATTTATCAAAACAACTTTTTCATTGCACTATGCATGGAAGACAATGGCTATGGTACTGTCAATTGTATCTCTCTTCCCTTTATGCCTGTCCACGACCTCTCAAAAAACAACATGGCTTCCGGTGCTGTTGGGATCTCTTGGATGCAAACCACTAACCATGTTTCTTATAACAGAAAACAAAATCTGGGGAAGGAAAAGTTGGCCCCTCAATGAAGGAATTATGGCTGTTGGAATAGTTAGCATTCTACTAAGTTCACTCCTCAAAAATGATGTGCCGCTAGCCGGCCCACTAATAGCTGGAGGCATGCTAATAGCATGTTATGTCATATCCGGAAGCTCAGCCGATTTATCACTGGAGAAAGCGGCTGAGGTCTCCTGGGAAGAAGAAGCAGAACACTCTGGTGCCTCACACAACATACTAGTGGAGGTCCAAGATGATGGAACCATGAAGATAAAAGATGAAGAGAGAGATGACACACTCACCATTCTCCTTAAAGCAACTCTGCTGGCAGTCTCAGGGGTGTACCCAATGTCAATACCAGCGACCCTTTTTGTGTGGTATTTTTGGCAGAAAAAGAAACAGAGATCAGGAGTGCTATGGGACACACCCAGCCCTCCAGAAGTGGAAAGAGCAGTTCTTGATGATGGTATCTATAGAATTTTGCAAAGAGGACTGTTGGGCAGGTCCCAAGTAGGAGTAGGAGTTTTCCAAGAAGGCGTGTTCCACACAATGTGGCACGTCACCAGGGGAGCTGTCCTCATGTATCAAGGGAAGAGGCTGGAACCAAGCTGGGCCAGTGTCAAAAAAGACTTGATCTCATATGGAGGAGGTTGGAGGTTTCAAGGATCCTGGAACACGGGAGAAGAAGTGCAGGTGATTGCTGTTGAACCGGGAAAAAACCCCAAAAATGTACAGACAGCGCCGGGCACCTTCAAGACCCCTGAAGGCGAAGTTGGAGCCATAGCCCTAGATTTTAAACCCGGCACATCTGGATCTCCCATCGTGAACAGAGAGGGAAAAATAGTAGGTCTTTATGGAAATGGAGTGGTGACAACAAGTGGAACCTACGTCAGTGCCATAGCTCAAGCTAAAGCATCACAAGAAGGGCCTCTACCAGAGATTGAGGACGAGGTGTTTAGGAAAAGAAACTTAACAATAATGGACCTACATCCAGGATCGGGAAAAACAAGAAGATATCTTCCAGCCATAGTCCGTGAGGCCATAAAAAGGAAGCTGCGCACGCTAATCTTGGCTCCCACAAGAGTTGTCGCTTCTGAAATGGCAGAGGCGCTCAAGGGAATGCCAATAAGGTATCAGACAACAGCAGTGAAGAGTGAACACACAGGAAAGGAGATAGTTGACCTTATGTGCCACGCCACTTTCACCATGCGTCTCCTGTCTCCCGTGAGAGTTCCCAATTACAACATGATTATCATGGATGAAGCACATTTCACCGATCCAGCCAGCATAGCGGCCAGAGGGTACATCTCAACCCGAGTGGGTATGGGTGAAGCAGCTGCGATCTTTATGACAGCCACTCCCCCAGGATCGGTGGAGGCCTTTCCACAGAGCAATGCAGTTATCCAAGATGAGGAAAGAGACATTCCTGAGAGATCATGGAACTCAGGCTATGACTGGATCACTGATTTCCCAGGTAAAACAGTCTGGTTTGTTCCAAGCATCAAATCAGGAAATGACATTGCCAACTGTTTAAGAAAGAACGGGAAACGGGTGATCCAATTGAGCAGAAAAACCTTTGACACTGAGTACCAGAAAACAAAAAACAACGACTGGGACTATGTCGTCACAACAGACATTTCCGAAATGGGAGCAAACTTCCGGGCCGACAGGGTAATAGACCCAAGGCGGTGTCTGAAACCGGTAATACTAAAAGATGGTCCAGAGCGCGTCATTCTAGCCGGACCGATGCCAGTGACTGTGGCCAGTGCCGCCCAGAGGAGAGGAAGAATTGGAAGGAACCAAAACAAGGAAGGTGATCAGTATATTTACATGGGACAGCCTTTAAACAATGATGAGGACCACGCTCATTGGACAGAAGCAAAAATGCTCCTTGACAATATAAACACACCAGAAGGGATTATCCCAGCCCTCTTTGAGCCGGAGAGAGAAAAGAGTGCAGCAATAGACGGGGAATACAGACTGCGGGGTGAAGCAAGGAAAACGTTCGTGGAGCTCATGAGAAGAGGAGATCTACCTGTCTGGCTATCCTACAAAGTTGCCTCAGAAGGCTTCCAGTACTCCGACAGAAGGTGGTGCTTTGATGGGGAAAGGAACAACCAGGTGTTGGAGGAGAACATGGACGTGGAGATCTGGACAAAAGAAGGAGAAAGAAAGAAACTACGACCCCGCTGGTTGGATGCCAGAACATACTCTGACCCACTGGCTCTGCGCGAGTTTAAAGAGTTTGCAGCAGGAAGAAGAAGCGTCTCAGGTGACCTAATATTAGAAATAGGGAAACTTCCACAACATTTGACGCAAAGGGCCCAGAATGCTTTGGACAACTTGGTCATGTTGCACAATTCCGAACAAGGAGGAAAAGCCTATAGACATGCTATGGAAGAACTACCAGACACCATAGAAACGTTGATGCTCCTAGCTTTGATAGCTGTGTTGACTGGTGGAGTGACGCTGTTCTTCCTATCAGGAAGAGGTCTAGGGAAAACATCCATCGGCCTACTCTGCGTGATGGCCTCAAGCGTACTGTTATGGATGGCCAGTGTGGAGCCCCATTGGATAGCGGCCTCCATCATACTGGAGTTCTTTCTGATGGTGCTGCTTATTCCAGAGCCAGACAGACAGCGCACTCCACAGGACAACCAGCTAGCATATGTGGTGATAGGTTTGTTATTCATGATATTGACAGTGGCAGCCAATGAGATGGGATTATTGGAAACCACAAAGAAAGACCTGGGGATTGGCCATGTAGCTGCTGAAAACCACCACCATGCTACAATGCTGGACGTAGACCTACATCCAGCTTCAGCCTGGACCCTCTATGCAGTGGCCACAACAATTATCACTCCCATGATGAGACACACAATTGAAAACACAACGGCAAATATTTCCCTGACAGCTATTGCAAACCAGGCAGCTATATTGATGGGACTTGACAAGGGATGGCCAATATCGAAGATGGACATAGGAGTTCCACTTCTCGCCTTGGGGTGCTATTCCCAGGTGAACCCGCTGACGCTGACAGCGGCGGTATTGATGCTAGTGGCTCATTACGCCATAATTGGACCTGGACTGCAAGCAAAAGCTACTAGAGAAGCTCAAAAAAGGACAGCGGCCGGAATAATGAAAAATCCAACTGTCGACGGGATTGTTGCAATAGATTTGGATCCTGTGGTTTACGATGCAAAATTTGAAAAACAGCTAGGCCAAATAATGTTGTTGATACTTTGCACATCACAGATTCTCTTGATGCGGACTACATGGGCCTTGTGTGAATCCATCACACTGGCTACTGGACCTCTGACCACTCTTTGGGAGGGATCTCCAGGAAAATTCTGGAACACCACGATAGCGGTGTCCATGGCAAACATTTTCAGGGGAAGTTATCTAGCAGGAGCAGGTCTGGCCTTCTCATTAATGAAATCTCTAGGAGGAGGTAGGAGAGGCACGGGAGCCCAAGGGGAAACACTGGGAGAAAAATGGAAAAGACAGCTAAACCAACTGAGCAAGTCAGAATTCAACACTTACAAAAGGAGTGGGATTATGGAGGTGGATAGATCCGAAGCCAAAGAGGGACTGAAAAGAGGAGAAACAACCAAACATGCAGTGTCGAGAGGAACAGCCAAACTGAGGTGGTTTGTGGAGAGGAACCTTGTGAAACCAGAAGGGAAAGTCATAGACCTCGGTTGTGGAAGAGGTGGCTGGTCATATTATTGCGCTGGGCTGAAGAAAGTCACAGAAGTGAAAGGATACACAAAAGGAGGACCTGGACATGAGGAACCAATCCCAATGGCGACCTATGGATGGAACCTAGTAAAGCTACACTCCGGAAAAGATGTATTCTTTACACCACCTGAGAAATGTGACACCCTTTTGTGTGATATTGGTGAGTCCTCTCCGAACCCAACTATAGAAGAAGGAAGAACGTTACGTGTTCTAAAGATGGTGGAACCATGGCTCAGAGGAAACCAATTTTGCATAAAAATTCTAAATCCCTATATGCCGAGTGTGGTAGAAACTCTGGAGCAAATGCAAAGAAAACATGGAGGAATGCTAGTGCGAAACCCACTCTCAAGAAATTCCACCCATGAAATGTACTGGGTTTCATGTGGAACAGGAAACATTGTGTCAGCAGTAAACATGACATCTAGAATGTTGCTAAATCGATTCACAATGGCTCACAGGAAGCCAACATATGAAAGAGACGTGGACTTAGGCGCTGGAACAAGACATGTGGCAGTGGAACCAGAGGTAGCCAACCTAGATATCATTGGCCAGAGGATAGAGAATATAAAAAATGAACATAAGTCAACATGGCATTATGATGAGGACAATCCATACAAAACATGGGCCTATCATGGATCATATGAGGTCAAGCCATCAGGATCAGCCTCATCCATGGTCAATGGCGTGGTGAGATTGCTCACCAAACCATGGGATGTTATCCCCATGGTCACACAAATAGCCATGACTGACACCACACCCTTTGGACAACAGAGGGTGTTTAAAGAGAAAGTTGACACGCGCACACCAAAAGCAAAACGAGGCACAGCACAAATTATGGAGGTGACAGCCAGGTGGTTATGGGGTTTCCTTTCTAGAAACAAAAAACCCAGAATCTGCACAAGAGAGGAGTTCACAAGAAAAGTTAGGTCAAACGCAGCTATTGGAGCAGTGTTCGTTGATGAAAATCAATGGAACTCAGCAAAAGAAGCAGTGGAAGACGAACGGTTCTGGGACCTTGTGCACAGAGAGAGGGAGCTTCATAAACAGGGAAAATGTGCCACGTGTGTCTACAATATGATGGGGAAGAGAGAGAAAAAATTAGGAGAGTTCGGAAAGGCAAAAGGAAGTCGTGCAATATGGTACATGTGGTTGGGAGCACGCTTTCTAGAGTTCGAAGCCCTTGGTTTCATGAATGAAGATCACTGGTTCAGTAGAGAGAATTCACTCAGTGGAGTGGAAGGAGAAGGACTCCACAAACTTGGATACATACTCAGAGACATATCAAAGATTCCAGGGGGAAATATGTATGCAGATGACACAGCCGGATGGGACACAAGAATAACAGAGGATGATCTTCAGAATGAGGCTAAAATCACTGACATCATGGAGCCCGAACATGCCCTATTGGCTACGTCAATCTTTAAGCTGACCTACCAAAATAAGGTGGTAAGGGTGCAGAGACCAGCAAAAAATGGAACCGTGATGGATGTTATATCCAGACGTGACCAGAGAGGAAGTGGACAGGTCGGAACTTATGGCTTAAACACTTTCACCAACATGGAGGCCCAACTAATAAGACAAATGGAGTCTGAGGGAATCTTTTTACCCAGCGAATTGGAAACCCCAAATCTAGCCGAAAGAGTTCTCGACTGGTTGGAAAAACATGGCGTCGAAAGGCTGAAAAGAATGGCAATCAGCGGAGATGACTGTGTGGTGAAACCAATTGATGACAGGTTCGCAACAGCCTTAACAGCTTTGAATGACATGGGAAAAGTAAGAAAAGACATACCGCAATGGGAACCTTCAAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGTTCACACCATTTCCACCAGCTGATTATGAAGGATGGGAGGGAGATAGTGGTGCCATGCCGCAACCAAGATGAACTTGTGGGTAGGGCCAGAGTATCACAAGGCGCCGGATGGAGCCTGAGAGAAACTGCATGCCTAGGCAAGTCATATGCACAAATGTGGCAGCTGATGTACTTCCACAGGAGAGACCTGAGACTAGCGGCTAATGCTATCTGTTCAGCCGTTCCAGTTGATTGGGTCCCAACCAGCCGCACCACCTGGTCGATCCATGCCCATCACCAATGGATGACAACAGAAGACATGTTATCAGTGTGGAATAGGGTTTGGATAGAGGAAAACCCATGGATGGAGGATAAAACTCATGTATCCAGTTGGGAAGATGTTCCATACTTAGGAAAAAGGGAAGATCAGTGGTGTGGATCCCTGATAGGCTTAACAGCAAGGGCCACCTGGGCCACTAACATACAAGTGGCCATAAACCAAGTGAGAAGGCTCATTGGGAATGAGAATTATCTAGATTACATGACATCAATGAAGAGATTCAAGAATGAGAGTGATCCCGAAGGGGCACTCTGGTAAGTCAACACATTCACAAAATAAAGGAAAATAAAAAATCAAACAAGGCAAGAAGTCAGGCCGGATTAAGCCATAGTACGGTAAGAGCTATGCTGCCTGTGAGCCCCGTCCAAGGACGTAAAATGAAGTCAGGCCGAAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTGGCTCCATCGTGGGGATGTAAAAACCCGGGAGGCTGCAACCCATGGAAGCTGTACGCATGGGGTAGCAGACTAGTGGTTAGAGGAGACCCCTCCCAAGACACAACGCAGCAGCGGGGCCCAACACCAGGGGAAGCTGTACCCTGGTGGTAAGGACTAGAGGTTAGAGGAGACCCCCCGCACAACAATAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCTACAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/datasets/denv1/tree.json b/nextclade/datasets/denv1/tree.json index cbad454d..86fd9c53 100644 --- a/nextclade/datasets/denv1/tree.json +++ b/nextclade/datasets/denv1/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Real-time tracking of dengue virus evolution", "updated": "2024-05-25", "build_url": "https://github.com/nextstrain/dengue", "maintainers": [{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": true, "color_by": "clade_membership"}, "genome_annotations": {"nuc": {"end": 10735, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/config/reference_denv1_genome.gb"}, "2K": {"end": 6826, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 6758, "strand": "+", "type": "CDS"}, "C": {"end": 436, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 95, "strand": "+", "type": "CDS"}, "E": {"end": 2419, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 935, "strand": "+", "type": "CDS"}, "M": {"end": 934, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 437, "strand": "+", "type": "CDS"}, "NS1": {"end": 3475, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 2420, "strand": "+", "type": "CDS"}, "NS2A": {"end": 4129, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 3476, "strand": "+", "type": "CDS"}, "NS2B": {"end": 4519, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 4130, "strand": "+", "type": "CDS"}, "NS3": {"end": 6376, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 4520, "strand": "+", "type": "CDS"}, "NS4A": {"end": 6757, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 6377, "strand": "+", "type": "CDS"}, "NS4B": {"end": 7573, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 6827, "strand": "+", "type": "CDS"}, "NS5": {"end": 10270, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 7574, "strand": "+", "type": "CDS"}, "pr": {"end": 709, "seqid": "../phylogenetic/config/reference_denv1_genome.gb", "start": 437, "strand": "+", "type": "CDS"}}, "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Israel", "#5E1D9D"], ["Saudi Arabia", "#581EA2"], ["Pakistan", "#4E21AC"], ["India", "#4929B5"], ["Sri Lanka", "#472EB9"], ["Nepal", "#4432BD"], ["Myanmar", "#403BC5"], ["Thailand", "#4040C6"], ["Malaysia", "#3F45C8"], ["Laos", "#3F4BCA"], ["Singapore", "#3F50CC"], ["China", "#3F56CE"], ["Cambodia", "#3E5BD0"], ["Vietnam", "#3F60D0"], ["Indonesia", "#4065CF"], ["Taiwan", "#426FCE"], ["Philippines", "#4274CE"], ["South Korea", "#447DCC"], ["Japan", "#4681C9"], ["French Polynesia", "#4885C7"], ["Australia", "#4B8DC2"], ["Papua New Guinea", "#4C91BF"], ["Fiji", "#59A3AA"], ["Gambia", "#5BA6A7"], ["Senegal", "#5DA8A3"], ["Mauritania", "#60AA9F"], ["C\u00f4te d'Ivoire", "#63AC9A"], ["Burkina Faso", "#65AD96"], ["Ghana", "#68AF92"], ["Benin", "#6BB18E"], ["Nigeria", "#6EB38A"], ["Gabon", "#71B486"], ["Cameroon", "#74B582"], ["Republic of the Congo", "#78B67E"], ["Angola", "#7BB77A"], ["Democratic Republic of the Congo", "#7EB976"], ["Tanzania", "#81BA72"], ["Kenya", "#85BA6F"], ["Djibouti", "#8CBC68"], ["Union of the Comoros", "#90BC65"], ["Somalia", "#98BD5E"], ["Seychelles", "#9BBE5B"], ["United Kingdom", "#ABBD52"], ["France", "#AFBD4F"], ["Germany", "#B2BD4D"], ["Italy", "#B6BD4B"], ["Argentina", "#C1BA47"], ["Chile", "#C8B944"], ["Paraguay", "#CBB742"], ["Bolivia", "#CEB541"], ["Brazil", "#D1B440"], ["Peru", "#D3B23F"], ["Ecuador", "#D6B03E"], ["Colombia", "#D9AE3E"], ["Venezuela", "#DFA53B"], ["Trinidad and Tobago", "#E0A13A"], ["Costa Rica", "#E59738"], ["Nicaragua", "#E68E36"], ["Saint Vincent and the Grenadines", "#E68935"], ["El Salvador", "#E67F33"], ["Honduras", "#E67A32"], ["Guatemala", "#E56E30"], ["Guadeloupe", "#E4682F"], ["Saint Barth\u00e9lemy", "#E25B2C"], ["Saint Martin", "#E1552B"], ["Jamaica", "#E04E2A"], ["Dominican Republic", "#E04828"], ["Haiti", "#DF4227"], ["Mexico", "#DE3B26"], ["Cuba", "#DD3525"], ["Bahamas", "#DC2E24"], ["USA", "#DB2823"]]}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["Asia", "#447CCD"], ["Oceania", "#5EA9A1"], ["Africa", "#8ABB6A"], ["Europe", "#BEBB48"], ["South America", "#E29E39"], ["North America", "#E2562B"]]}, {"key": "genotype_nextclade", "title": "Dengue Genotype (Nextclade)", "type": "categorical", "scale": [["DENV1/I", "#4784C8"], ["DENV1/II", "#67AE95"], ["DENV1/III", "#98BD5E"], ["DENV1/IV", "#CDB642"], ["DENV1/V", "#E68634"]]}, {"key": "serotype_genbank", "title": "Serotype (Genbank metadata)", "type": "categorical", "scale": [["denv1", "#4C90C0"]]}, {"key": "clade_membership", "title": "Dengue Genotype 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"AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGAATCGGAAGCTTGCTTAACGTAGTTCTAACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGTCGACCGTCTTTCAATATGCTGAAACGCGCGAGAAACCGCGTGTCAACTGTTTCACAGTTGGCGAAGAGATTCTCAAAAGGATTGCTTTCAGGCCAAGGACCCATGAAATTGGTGATGGCTTTTATAGCATTCCTAAGATTTCTAGCCATACCTCCAACAGCAGGAATTTTGGCTAGATGGGGCTCATTCAAGAAGAATGGAGCGATCAAAGTGTTACGGGGTTTCAAGAAAGAAATCTCAAACATGTTGAACATAATGAACAGGAGGAAAAGATCTGTGACCATGCTCCTCATGCTGCTGCCCACAGCCCTGGCGTTCCATCTGACCACCCGAGGGGGAGAGCCGCACATGATAGTTAGCAAGCAGGAAAGAGGAAAATCACTTTTGTTTAAGACCTCTGCAGGTGTCAACATGTGCACCCTTATTGCAATGGATTTGGGAGAGTTATGTGAGGACACAATGACCTACAAATGCCCCCGGATCACTGAGACGGAACCAGATGACGTTGACTGTTGGTGCAATGCCACGGAGACATGGGTGACCTATGGAACATGTTCTCAAACTGGTGAACACCGACGAGACAAACGTTCCGTCGCACTGGCACCACACGTAGGGCTTGGTCTAGAAACAAGAACCGAAACGTGGATGTCCTCTGAAGGCGCTTGGAAACAAATACAAAAAGTGGAGACCTGGGCTCTGAGACACCCAGGATTCACGGTGATAGCCCTTTTTCTAGCACATGCCATAGGAACATCCATCACCCAGAAAGGGATCATTTTTATTTTGCTGATGCTGGTAACTCCATCCATGGCCATGCGGTGCGTGGGAATAGGCAACAGAGACTTCGTGGAAGGACTGTCAGGAGCTACGTGGGTGGATGTGGTACTGGAGCATGGAAGTTGCGTCACTACCATGGCAAAAGACAAACCAACACTGGACATTGAACTCTTGAAGACGGAGGTCACAAACCCTGCCGTCCTGCGCAAACTGTGCATTGAAGCTAAAATATCAAACACCACCACCGATTCGAGATGTCCAACACAAGGAGAAGCCACGCTGGTGGAAGAACAGGACACGAACTTTGTGTGTCGACGAACGTTCGTGGACAGAGGCTGGGGCAATGGTTGTGGGCTATTCGGAAAAGGTAGCTTAATAACGTGTGCTAAGTTTAAGTGTGTGACAAAACTGGAAGGAAAGATAGTCCAATATGAAAACTTAAAATATTCAGTGATAGTCACCGTACACACTGGAGACCAGCACCAAGTTGGAAATGAGACCACAGAACATGGAACAACTGCAACCATAACACCTCAAGCTCCCACGTCGGAAATACAGCTGACAGACTACGGAGCTCTAACATTGGATTGTTCACCTAGAACAGGGCTAGACTTTAATGAGATGGTGTTGTTGACAATGAAAAAAAAATCATGGCTCGTCCACAAACAATGGTTTCTAGACTTACCACTGCCTTGGACCTCGGGGGCTTCAACATCCCAAGAGACTTGGAATAGACAAGACTTGCTGGTCACATTTAAGACAGCTCATGCAAAAAAGCAGGAAGTAGTCGTACTAGGATCACAAGAAGGAGCAATGCACACTGCGTTGACTGGAGCGACAGAAATCCAAACGTCTGGAACGACAACAATTTTTGCAGGACACCTGAAATGCAGATTAAAAATGGATAAACTGATTTTAAAAGGGATGTCATATGTAATGTGCACAGGGTCATTCAAGTTAGAGAAGGAAGTGGCTGAGACCCAGCATGGAACTGTTCTAGTGCAGGTTAAATACGAAGGAACAGATGCACCATGCAAGATCCCCTTCTCGTCCCAAGATGAGAAGGGAGTAACCCAGAATGGGAGATTGATAACAGCCAACCCCATAGTCACTGACAAAGAAAAACCAGTCAACATTGAAGCGGAGCCACCTTTTGGTGAGAGCTACATTGTGGTAGGAGCAGGTGAAAAAGCTTTGAAACTAAGCTGGTTCAAGAAGGGAAGCAGTATAGGGAAAATGTTTGAAGCAACTGCCCGTGGAGCACGAAGGATGGCCATCCTGGGAGACACTGCATGGGACTTCGGTTCTATAGGAGGGGTGTTCACGTCTGTGGGAAAACTGATACACCAGATTTTTGGGACTGCGTATGGAGTTTTGTTCAGCGGTGTTTCTTGGACCATGAAGATAGGAATAGGGATTCTGCTGACATGGCTAGGATTAAACTCAAGGAGCACGTCCCTTTCAATGACGTGTATCGCAGTTGGCATGGTCACACTGTACCTAGGAGTCATGGTTCAGGCGGACTCGGGATGTGTAATCAACTGGAAAGGCAGAGAACTCAAATGTGGAAGCGGCATTTTTGTCACCAATGAAGTCCACACCTGGACAGAGCAATATAAATTCCAGGCCGACTCCCCTAAGAGACTATCAGCGGCCATTGGGAAGGCATGGGAGGAGGGTGTGTGTGGAATTCGATCAGCCACTCGTCTCGAGAACATCATGTGGAAGCAAATATCAAATGAATTAAACCACATCTTACTTGAAAATGACATGAAATTTACAGTGGTCGTAGGAGACGTTAGTGGAATCTTGGCCCAAGGAAAGAAAATGATTAGGCCACAACCCATGGAACACAAATACTCGTGGAAAAGCTGGGGAAAAGCCAAAATCATAGGAGCAGATGTACAGAATACCACCTTCATCATCGACGGCCCAAACACCCCAGAATGCCCTGATAACCAAAGAGCATGGAACATTTGGGAAGTTGAAGACTATGGATTTGGAATTTTCACGACAAACATATGGTTGAAATTGCGTGACTCCTACACTCAAGTGTGTGACCACCGGCTAATGTCAGCTGCCATCAAGGATAGCAAAGCAGTCCATGCTGACATGGGGTACTGGATAGAAAGTGAAAAGAACGAGACTTGGAAGTTGGCAAGAGCCTCCTTCATAGAAGTTAAGACATGCATCTGGCCAAAATCCCACACTCTATGGAGCAATGGAGTCCTGGAAAGTGAGATGATAATCCCAAAGATATATGGAGGACCAATATCTCAGCACAACTACAGACCAGGATATTTCACACAAACAGCAGGGCCGTGGCACTTGGGCAAGTTAGAACTAGATTTTGATTTATGTGAAGGTACCACTGTTGTTGTGGATGAACATTGTGGAAATCGAGGACCATCTCTTAGAACCACAACAGTCACAGGAAAGACAATCCATGAATGGTGCTGTAGATCTTGCACGTTACCCCCCCTACGTTTCAAAGGAGAAGACGGGTGCTGGTACGGCATGGAAATCAGACCAGTCAAGGAGAAGGAAGAGAACCTAGTTAAGTCAATGGTCTCTGCAGGGTCAGGAGAAGTGGACAGTTTTTCACTAGGACTGCTATGCATATCAATAATGATCGAAGAGGTAATGAGATCCAGATGGAGCAGAAAAATGCTGATGACTGGAACATTGGCTGTGTTCCTCCTTCTCACAATGGGACAATTGACATGGAATGATCTGATCAGGCTATGTATCATGGTTGGAGCCAACGCTTCAGACAAGATGGGGATGGGAACAACGTACCTAGCTTTGATGGCCACTTTCAGAATGAGACCAATGTTCGCAGTCGGGCTACTGTTTCGCAGATTAACATCTAGAGAAGTTCTTCTTCTTACAGTTGGATTGAGTCTGGTGGCATCTGTAGAACTACCAAATTCCTTAGAGGAGCTAGGGGATGGACTTGCAATGGGCATCATGATGTTGAAATTACTGACTGATTTTCAGTCACATCAGCTATGGGCTACCTTGCTGTCTTTAACATTTGTCAAAACAACTTTTTCATTGCACTATGCATGGAAGACAATGGCTATGATACTGTCAATTGTATCTCTCTTCCCTTTATGCCTGTCCACGACTTCTCAAAAAACAACATGGCTTCCGGTGTTGCTGGGATCTCTTGGATGCAAACCACTAACCATGTTTCTTATAACAGAAAACAAAATCTGGGGAAGGAAAAGCTGGCCTCTCAATGAAGGAATTATGGCTGTTGGAATAGTTAGCATTCTTCTAAGTTCACTTCTCAAGAATGATGTGCCACTAGCTGGCCCACTAATAGCTGGAGGCATGCTAATAGCATGTTATGTCATATCTGGAAGCTCGGCCGATTTATCACTGGAGAAAGCGGCTGAGGTCTCCTGGGAAGAAGAAGCAGAACACTCTGGTGCCTCACACAACATACTAGTGGAGGTCCAAGATGATGGAACCATGAAGATAAAGGATGAAGAGAGAGATGACACACTCACCATTCTCCTCAAAGCAACTCTGCTAGCAATCTCAGGGGTATACCCAATGTCAATACCGGCGACCCTCTTTGTGTGGTATTTTTGGCAGAAAAAGAAACAGAGATCAGGAGTGCTATGGGACACACCCAGCCCTCCAGAAGTGGAAAGAGCAGTCCTTGATGATGGCATTTATAGAATTCTCCAAAGAGGATTGTTGGGCAGGTCTCAAGTAGGAGTAGGAGTTTTTCAAGAAGGCGTGTTCCACACAATGTGGCACGTCACCAGGGGAGCTGTCCTCATGTACCAAGGGAAGAGACTGGAACCAAGTTGGGCCAGTGTCAAAAAAGACTTGATCTCATATGGAGGAGGTTGGAGGTTTCAAGGATCCTGGAACGCGGGAGAAGAAGTGCAGGTGATTGCTGTTGAACCGGGGAAGAACCCCAAAAATGTACAGACAGCGCCGGGTACCTTCAAGACCCCTGAAGGCGAAGTTGGAGCCATAGCTCTAGACTTTAAACCCGGCACATCTGGATCTCCTATCGTGAACAGAGAGGGAAAAATAGTAGGTCTTTATGGAAATGGAGTGGTGACAACAAGTGGTACCTACGTCAGTGCCATAGCTCAAGCTAAAGCATCACAAGAAGGGCCTCTACCAGAGATTGAGGACGAGGTGTTTAGGAAAAGAAACTTAACAATAATGGACCTACATCCAGGATCGGGAAAAACAAGAAGATACCTTCCAGCCATAGTCCGTGAGGCCATAAAAAGAAAGCTGCGCACGCTAGTCTTAGCTCCCACAAGAGTTGTCGCTTCTGAAATGGCAGAGGCGCTCAAGGGAATGCCAATAAGGTATCAGACAACAGCAGTGAAGAGTGAACACACGGGAAAGGAGATAGTTGACCTTATGTGTCACGCCACTTTCACTATGCGTCTCCTGTCTCCTGTGAGAGTTCCCAATTATAATATGATTATCATGGATGAAGCACATTTTACCGATCCAGCCAGCATAGCAGCCAGAGGGTATATCTCAACCCGAGTGGGTATGGGTGAAGCAGCTGCGATTTTCATGACAGCCACTCCCCCCGGATCGGTGGAGGCCTTTCCACAGAGCAATGCAGTTATCCAAGATGAGGAAAGAGACATTCCTGAAAGATCATGGAACTCAGGCTATGACTGGATCACTGATTTCCCAGGTAAAACAGTCTGGTTTGTTCCAAGCATCAAATCAGGAAATGACATTGCCAACTGTTTAAGAAAGAATGGGAAACGGGTGGTCCAATTGAGCAGAAAAACTTTTGACACTGAGTACCAGAAAACAAAAAATAACGACTGGGACTATGTTGTCACAACAGACATATCCGAAATGGGAGCAAACTTCCGAGCCGACAGGGTAATAGACCCGAGGCGGTGCCTGAAACCGGTAATACTAAAAGATGGCCCAGAGCGTGTCATTCTAGCCGGACCGATGCCAGTGACTGTGGCTAGCGCCGCCCAGAGGAGAGGAAGAATTGGAAGGAACCAAAATAAGGAAGGCGATCAGTATATTTACATGGGACAGCCTCTAAACAATGATGAGGACCACGCCCATTGGACAGAAGCAAAAATGCTCCTTGACAACATAAACACACCAGAAGGGATTATCCCAGCCCTCTTTGAGCCGGAGAGAGAAAAGAGTGCAGCAATAGACGGGGAATACAGACTACGGGGTGAAGCGAGGAAAACGTTCGTGGAGCTCATGAGAAGAGGAGATCTACCTGTCTGGCTATCCTACAAAGTTGCCTCAGAAGGCTTCCAGTACTCCGACAGAAGGTGGTGCTTTGATGGGGAAAGGAACAACCAGGTGTTGGAGGAGAACATGGACGTGGAGATCTGGACAAAAGAAGGAGAAAGAAAGAAACTACGACCCCGCTGGCTGGATGCCAGAACATACTCTGACCCACTGGCTCTGCGCGAATTCAAAGAGTTCGCAGCAGGAAGAAGAAGCGTCTCAGGTGACCTAATATTAGAAATAGGGAAACTTCCACAACATTTAACGCAAAGGGCCCAGAACGCCTTGGACAATCTGGTTATGTTGCACAACTCTGAACAAGGAGGAAAAGCCTATAGACACGCCATGGAAGAACTACCAGACACCATAGAAACGTTAATGCTCCTAGCTTTGATAGCTGTGCTGACTGGTGGAGTGACGTTGTTCTTCCTATCAGGAAGGGGTCTAGGAAAAACATCCATTGGCCTACTCTGCGTGATTGCCTCAAGTGCACTGTTATGGATGGCCAGTGTGGAACCCCATTGGATAGCGGCCTCTATCATACTGGAGTTCTTTCTGATGGTGTTGCTTATTCCAGAGCCGGACAGACAGCGCACTCCACAAGACAACCAGCTAGCATACGTGGTGATAGGTCTGTTATTCATGATATTGACAGTGGCAGCCAATGAGATGGGATTACTGGAAACCACAAAGAAGGACCTGGGGATTGGTCATGCAGCTGCTGAAAACCACCATCATGCTGCAATGCTGGACGTAGACCTACATCCAGCTTCAGCCTGGACTCTCTATGCAGTGGCCACAACAATTATCACTCCCATGATGAGACACACAATTGAAAACACAACGGCAAATATTTCCCTGACAGCTATTGCAAACCAGGCAGCTATATTGATGGGACTTGACAAGGGATGGCCAATATCAAAGATGGACATAGGAGTTCCACTTCTCGCCTTGGGGTGCTATTCTCAGGTGAACCCGCTGACGCTGACAGCGGCGGTATTGATGCTAGTGGCTCATTATGCCATAATTGGACCCGGACTGCAAGCAAAAGCTACTAGAGAAGCTCAAAAAAGGACAGCAGCCGGAATAATGAAAAACCCAACTGTCGACGGGATCGTTGCAATAGATTTGGACCCTGTGGTTTACGATGCAAAATTTGAAAAACAGCTAGGCCAAATAATGTTGTTGATACTTTGCACATCACAGATCCTCCTGATGCGGACCACATGGGCCTTGTGTGAATCCATCACACTAGCCACTGGACCTCTGACTACGCTTTGGGAGGGATCTCCAGGAAAATTCTGGAACACCACGATAGCGGTGTCCATGGCAAACATTTTTAGGGGAAGTTATCTAGCAGGAGCAGGTCTGGCCTTTTCATTAATGAAATCTCTAGGAGGAGGTAGGAGAGGCACGGGAGCCCAAGGGGAAACACTGGGAGAAAAATGGAAAAGACAGCTAAACCAATTGAGCAAGTCAGAATTCAACACTTACAAAAGGAGTGGGATTATAGAGGTGGATAGATCTGAAGCCAAAGAGGGGTTAAAAAGAGGAGAAACGACTAAACACGCAGTGTCGAGAGGAACGGCCAAACTGAGGTGGTTTGTGGAGAGGAACCTTGTGAAACCAGAAGGGAAAGTCATAGACCTCGGTTGTGGAAGAGGTGGCTGGTCATATTATTGCGCTGGGCTGAAGAAAGTCACAGAAGTGAAAGGATACACGAAAGGAGGACCTGGACATGAGGAACCAATCCCAATGGCAACCTATGGATGGAACCTAGTAAAGCTATACTCCGGGAAAGATGTATTCTTTACACCACCTGAGAAATGTGACACCCTCTTGTGTGATATTGGTGAGTCCTCTCCGAACCCAACTATAGAAGAAGGAAGAACGTTACGTGTTCTAAAGATGGTGGAACCATGGCTCAGAGGAAACCAATTTTGCATAAAAATTCTAAATCCCTATATGCCGAGTGTGGTAGAAACTTTGGAGCAAATGCAAAGAAAACATGGAGGAATGCTAGTGCGAAATCCACTCTCAAGAAACTCCACTCATGAAATGTACTGGGTTTCATGTGGAACAGGAAACATTGTGTCAGCAGTAAACATGACATCTAGAATGCTGCTAAATCGATTCACAATGGCTCACAGGAAGCCAACATATGAAAGAGACGTGGACTTAGGCGCTGGAACAAGACATGTGGCAGTAGAACCAGAGGTGGCCAACCTAGATATCATTGGCCAGAGGATAGAGAATATAAAAAATGAACACAAATCAACATGGCATTATGATGAGGACAATCCATACAAAACATGGGCCTATCATGGATCATATGAGGTCAAGCCATCAGGATCAGCCTCATCCATGGTCAATGGTGTGGTGAGACTGCTAACCAAACCATGGGATGTCATTCCCATGGTCACACAAATAGCCATGACTGACACCACACCCTTTGGACAACAGAGGGTGTTTAAAGAGAAAGTTGACACGCGTACACCAAAAGCGAAACGAGGCACAGCACAAATTATGGAGGTGACAGCCAGGTGGTTATGGGGTTTTCTCTCTAGAAACAAAAAACCCAGAATCTGCACAAGAGAGGAGTTCACAAGAAAAGTCAGGTCAAACGCAGCTATTGGAGCAGTGTTCGTTGATGAAAATCAATGGAACTCAGCAAAAGAGGCAGTGGAAGATGAACGGTTCTGGGACCTTGTGCACAGAGAGAGGGAGCTTCATAAACAAGGAAAATGTGCCACGTGTGTCTACAACATGATGGGAAAGAGAGAGAAAAAATTAGGAGAGTTCGGAAAGGCAAAAGGAAGTCGCGCAATATGGTACATGTGGTTGGGAGCGCGCTTTTTAGAGTTTGAAGCCCTTGGTTTCATGAATGAAGATCACTGGTTCAGCAGAGAGAATTCACTCAGTGGAGTGGAAGGAGAAGGACTCCACAAACTTGGATACATACTCAGAGACATATCAAAGATTCCAGGGGGAAATATGTATGCAGATGACACAGCCGGATGGGACACAAGAATAACAGAGGATGATCTTCAGAATGAGGCCAAAATCACTGACATCATGGAACCTGAACATGCCCTATTGGCCACGTCAATCTTTAAGCTAACCTACCAAAACAAGGTAGTAAGGGTGCAGAGACCAGCGAAAAATGGAACCGTGATGGATGTCATATCCAGACGTGACCAGAGAGGAAGTGGACAGGTTGGAACCTATGGCTTAAACACCTTCACCAACATGGAGGCCCAACTAATAAGACAAATGGAGTCTGAGGGAATCTTTTCACCCAGCGAATTGGAAACCCCAAATCTAGCCGAAAGAGTCCTCGACTGGTTGAAAAAACATGGCACCGAGAGGCTGAAAAGAATGGCAATCAGTGGAGATGACTGTGTGGTGAAACCAATCGATGACAGATTTGCAACAGCCTTAACAGCTTTGAATGACATGGGAAAGGTAAGAAAAGACATACCGCAATGGGAACCTTCAAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGTTCACACCATTTCCACCAGCTGATTATGAAGGATGGGAGGGAGATAGTGGTGCCATGCCGCAACCAAGATGAACTTGTAGGTAGGGCCAGAGTATCACAAGGCGCCGGATGGAGCTTGAGAGAAACTGCATGCCTAGGCAAGTCATATGCACAAATGTGGCAGCTGATGTACTTCCACAGGAGAGACTTGAGATTAGCGGCTAATGCTATCTGTTCAGCCGTTCCAGTTGATTGGGTCCCAACCAGCCGCACCACCTGGTCGATCCATGCCCACCATCAATGGATGACAACAGAAGACATGTTGTCAGTGTGGAATAGGGTTTGGATAGAGGAAAACCCATGGATGGAGGACAAGACTCATGTGTCCAGTTGGGAAGACGTTCCATACCTAGGAAAAAGGGAAGATCAATGGTGTGGTTCCCTAATAGGCTTAACAGCACGAGCCACCTGGGCCACCAACATACAAGTGGCCATAAACCAAGTGAGAAGGCTCATTGGGAATGAGAATTATCTAGACTTCATGACATCAATGAAGAGATTCAAAAACGAGAGTGATCCCGAAGGGGCACTCTGGTAAGCCAACTCATTCACAAAATAAAGGAAAATAAAAAATCAAACAAGGCAAGAAGTCAGGCCGGATTAAGCCATAGCACGGTAAGAGCTATGCTGCCTGTGAGCCCCGTCCAAGGACGTAAAATGAAGTCAGGCCGAAAGCCACGGTTCGAGCAAGCCGTGCTGCCTGTAGCTCCATCGTGGGGATGTAAAAACCCGGGAGGCTGCAAACCATGGAAGCTGTACGCATGGGGTAGCAGACTAGTGGTTAGAGGAGACCCCTCCCAAGACACAACGCAGCAGCGGGGCCCAACACCAGGGGAAGCTGTACCCTGGTGGTAAGGACTAGAGGTTAGAGGAGACCCCCCGCACAACAACAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCTACAGCATCATTCCAGGCACAGAACGCCAAAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT", "2K": "TPQDNQLAYVVIGLLFMILTVAA", "C": "MNNQRKKTGRPSFNMLKRARNRVSTVSQLAKRFSKGLLSGQGPMKLVMAFIAFLRFLAIPPTAGILARWGSFKKNGAIKVLRGFKKEISNMLNIMNRRKRSVTMLLMLLPTALA", "E": "MRCVGIGNRDFVEGLSGATWVDVVLEHGSCVTTMAKDKPTLDIELLKTEVTNPAVLRKLCIEAKISNTTTDSRCPTQGEATLVEEQDTNFVCRRTFVDRGWGNGCGLFGKGSLITCAKFKCVTKLEGKIVQYENLKYSVIVTVHTGDQHQVGNETTEHGTTATITPQAPTSEIQLTDYGALTLDCSPRTGLDFNEMVLLTMKKKSWLVHKQWFLDLPLPWTSGASTSQETWNRQDLLVTFKTAHAKKQEVVVLGSQEGAMHTALTGATEIQTSGTTTIFAGHLKCRLKMDKLILKGMSYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKGSSIGKMFEATARGARRMAILGDTAWDFGSIGGVFTSVGKLIHQIFGTAYGVLFSGVSWTMKIGIGILLTWLGLNSRSTSLSMTCIAVGMVTLYLGVMVQA", "M": "FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMTYKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVGLGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQKGIIFILLMLVTPSMA", "NS1": "DSGCVINWKGRELKCGSGIFVTNEVHTWTEQYKFQADSPKRLSAAIGKAWEEGVCGIRSATRLENIMWKQISNELNHILLENDMKFTVVVGDVSGILAQGKKMIRPQPMEHKYSWKSWGKAKIIGADVQNTTFIIDGPNTPECPDNQRAWNIWEVEDYGFGIFTTNIWLKLRDSYTQVCDHRLMSAAIKDSKAVHADMGYWIESEKNETWKLARASFIEVKTCIWPKSHTLWSNGVLESEMIIPKIYGGPISQHNYRPGYFTQTAGPWHLGKLELDFDLCEGTTVVVDEHCGNRGPSLRTTTVTGKTIHEWCCRSCTLPPLRFKGEDGCWYGMEIRPVKEKEENLVKSMVSA", "NS2A": "GSGEVDSFSLGLLCISIMIEEVMRSRWSRKMLMTGTLAVFLLLTMGQLTWNDLIRLCIMVGANASDKMGMGTTYLALMATFRMRPMFAVGLLFRRLTSREVLLLTVGLSLVASVELPNSLEELGDGLAMGIMMLKLLTDFQSHQLWATLLSLTFVKTTFSLHYAWKTMAMILSIVSLFPLCLSTTSQKTTWLPVLLGSLGCKPLTMFLITENKIWGRK", "NS2B": "SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSADLSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLKATLLAISGVYPMSIPATLFVWYFWQKKKQR", "NS3": "SGVLWDTPSPPEVERAVLDDGIYRILQRGLLGRSQVGVGVFQEGVFHTMWHVTRGAVLMYQGKRLEPSWASVKKDLISYGGGWRFQGSWNAGEEVQVIAVEPGKNPKNVQTAPGTFKTPEGEVGAIALDFKPGTSGSPIVNREGKIVGLYGNGVVTTSGTYVSAIAQAKASQEGPLPEIEDEVFRKRNLTIMDLHPGSGKTRRYLPAIVREAIKRKLRTLVLAPTRVVASEMAEALKGMPIRYQTTAVKSEHTGKEIVDLMCHATFTMRLLSPVRVPNYNMIIMDEAHFTDPASIAARGYISTRVGMGEAAAIFMTATPPGSVEAFPQSNAVIQDEERDIPERSWNSGYDWITDFPGKTVWFVPSIKSGNDIANCLRKNGKRVVQLSRKTFDTEYQKTKNNDWDYVVTTDISEMGANFRADRVIDPRRCLKPVILKDGPERVILAGPMPVTVASAAQRRGRIGRNQNKEGDQYIYMGQPLNNDEDHAHWTEAKMLLDNINTPEGIIPALFEPEREKSAAIDGEYRLRGEARKTFVELMRRGDLPVWLSYKVASEGFQYSDRRWCFDGERNNQVLEENMDVEIWTKEGERKKLRPRWLDARTYSDPLALREFKEFAAGRR", "NS4A": "SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPDTIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVIASSALLWMASVEPHWIAASIILEFFLMVLLIPEPDRQR", "NS4B": "NEMGLLETTKKDLGIGHAAAENHHHAAMLDVDLHPASAWTLYAVATTIITPMMRHTIENTTANISLTAIANQAAILMGLDKGWPISKMDIGVPLLALGCYSQVNPLTLTAAVLMLVAHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGIVAIDLDPVVYDAKFEKQLGQIMLLILCTSQILLMRTTWALCESITLATGPLTTLWEGSPGKFWNTTIAVSMANIFRGSYLAGAGLAFSLMKSLGGGRR", "NS5": "GTGAQGETLGEKWKRQLNQLSKSEFNTYKRSGIIEVDRSEAKEGLKRGETTKHAVSRGTAKLRWFVERNLVKPEGKVIDLGCGRGGWSYYCAGLKKVTEVKGYTKGGPGHEEPIPMATYGWNLVKLYSGKDVFFTPPEKCDTLLCDIGESSPNPTIEEGRTLRVLKMVEPWLRGNQFCIKILNPYMPSVVETLEQMQRKHGGMLVRNPLSRNSTHEMYWVSCGTGNIVSAVNMTSRMLLNRFTMAHRKPTYERDVDLGAGTRHVAVEPEVANLDIIGQRIENIKNEHKSTWHYDEDNPYKTWAYHGSYEVKPSGSASSMVNGVVRLLTKPWDVIPMVTQIAMTDTTPFGQQRVFKEKVDTRTPKAKRGTAQIMEVTARWLWGFLSRNKKPRICTREEFTRKVRSNAAIGAVFVDENQWNSAKEAVEDERFWDLVHRERELHKQGKCATCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGFMNEDHWFSRENSLSGVEGEGLHKLGYILRDISKIPGGNMYADDTAGWDTRITEDDLQNEAKITDIMEPEHALLATSIFKLTYQNKVVRVQRPAKNGTVMDVISRRDQRGSGQVGTYGLNTFTNMEAQLIRQMESEGIFSPSELETPNLAERVLDWLKKHGTERLKRMAISGDDCVVKPIDDRFATALTALNDMGKVRKDIPQWEPSKGWNDWQQVPFCSHHFHQLIMKDGREIVVPCRNQDELVGRARVSQGAGWSLRETACLGKSYAQMWQLMYFHRRDLRLAANAICSAVPVDWVPTSRTTWSIHAHHQWMTTEDMLSVWNRVWIEENPWMEDKTHVSSWEDVPYLGKREDQWCGSLIGLTARATWATNIQVAINQVRRLIGNENYLDFMTSMKRFKNESDPEGALW", "pr": 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"AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGAATCGGAAGCTTGCTTAACGTAGTTCTAACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGTCGACCGTCTTTCAATATGCTGAAACGCGCGAGAAACCGCGTGTCAACTGTTTCACAGTTGGCGAAGAGATTCTCAAAAGGATTGCTCTCAGGCCAAGGACCCATGAAATTGGTGATGGCTTTCATAGCATTCCTAAGATTTCTAGCCATACCCCCAACAGCAGGAATTTTGGCTAGATGGGGCTCATTCAAGAAGAATGGAGCGATTAAAGTGTTACGGGGTTTCAAGAAAGAAATCTCAAACATGTTGAACATAATGAACAGGAGGAAAAGATCCGTGACCATGCTCCTTATGCTGCTGCCCACAGCCCTGGCGTTCCATCTGACCACACGAGGGGGAGAGCCGCACATGATAGTTAGCAAGCAGGAAAGAGGAAAGTCACTTTTGTTTAAGACCTCTGCAGGTGTCAACATGTGCACCCTTATTGCGATGGATTTGGGAGAGTTATGTGAGGACACAATGACCTACAAATGCCCCCGGATCACTGAGGCGGAACCAGATGACGTTGACTGTTGGTGCAATGCCACGGACACATGGGTGACCTATGGAACGTGTTCTCAAACTGGCGAACACCGACGAGACAAACGTTCCGTCGCACTGGCCCCACACGTGGGGCTTGGTCTAGAAACAAGAACCGAAACGTGGATGTCCTCTGAAGGCGCTTGGAAACAAATACAAAAAGTGGAGACTTGGGCTCTGAGACACCCAGGATTCACGGTGATAGCCCTTTTTCTAGCACATGCCATAGGAACATCCATCACCCAGAAAGGGATTATTTTCATTTTGCTGATGCTGGTAACACCATCCATGGCCATGCGATGCGTGGGAATAGGCAACAGAGACTTCGTGGAAGGACTGTCAGGAGCAACGTGGGTGGATGTGGTACTGGAGCATGGAAGTTGCGTCACCACCATGGCAAAAAATAAACCAACATTGGACATTGAACTCTTGAAGACGGAGGTCACAAACCCTGCCGTCCTGCGCAAACTGTGCATTGAAGCTAAAATATCAAACACCACCACCGATTCAAGATGTCCAACACAAGGAGAAGCCACACTGGTGGAAGAACAAGACGCGAACTTTGTGTGTCGACGAACGTTCGTGGACAGAGGCTGGGGCAATGGCTGTGGGCTATTCGGAAAAGGTAGCCTAATAACGTGTGCTAAGTTCAAGTGTGTGACAAAACTAGAAGGAAAGATAGTTCAATATGAAAACTTAAAATATTCAGTGATAGTCACCGTCCACACTGGAGACCAGCACCAGGTGGGAAATGAGACCACAGAACATGGAACAACTGCAACCATAACACCTCAAGCTCCTACGTCGGAAATACAGCTGACCGACTACGGAGCCCTTACATTGGATTGCTCACCTAGAACAGGGCTAGACTTTAATGAGATGGTGTTGTTGACAATGAAAGAAAAATCATGGCTTGTCCACAAACAATGGTTTCTAGACTTACCACTGCCTTGGACCTCGGGGGCTTCAACATCCCAAGAGACTTGGAACAGACAAGATTTGCTGGTCACATTTAAGACAGCTCATGCAAAGAAGCAGGAAGTAGTCGTACTAGGATCACAAGAAGGAGCAATGCACACTGCGTTGACTGGAGCGACAGAAATCCAAACGTCAGGAACGACAACAATTTTTGCAGGACACCTGAAATGCAGACTAAAAATGGACAAACTGACTTTAAAAGGGATGTCATATGTGATGTGCACAGGCTCATTCAAGTTAGAGAAAGAAGTGGCTGAGACCCAGCATGGAACTGTTCTAGTGCAGGTTAAATACGAAGGAACAGATGCACCATGCAAGATCCCCTTTTCGACCCAAGATGAGAAAGGAGTAACCCAGAATGGGAGATTGATAACAGCCAACCCCATAGTCACTGACAAAGAAAAACCAGTCAACATTGAGGCAGAACCACCTTTTGGTGAGAGCTACATCGTGGTAGGAGCAGGTGAAAAAGCTTTGAAACTAAGCTGGTTCAAGAAAGGAAGCAGCATAGGGAAAATGTTTGAAGCAACTGCCCGAGGAGCACGAAGGATGGCCATCCTGGGAGACACCGCATGGGACTTCGGTTCTATAGGAGGAGTGTTCACGTCTGTGGGAAAACTGGTACACCAGGTTTTTGGAACTGCATATGGAGTTTTGTTCAGCGGTGTTTCTTGGACCATGAAAATAGGAATAGGGATTCTGCTGACATGGCTAGGATTAAATTCAAGGAGCACGTCCCTTTCGATGACGTGCATTGCAGTTGGCATGGTCACACTGTACCTAGGAGTCATGGTTCAGGCGGACTCGGGATGTGTAATCAACTGGAAAGGCAGAGAACTCAAATGTGGAAGTGGCATTTTTGTCACTAATGAAGTTCACACTTGGACAGAGCAATACAAATTCCAGGCTGACTCCCCAAAGAGACTATCAGCAGCCATTGGGAAGGCATGGGAGGAGGGTGTGTGTGGAATTCGATCAGCCACTCGTCTCGAGAACATCATGTGGAAGCAAATATCAAATGAATTGAACCACATCCTACTTGAAAATGACATGAAATTCACAGTGGTCGTAGGAGATGTTAGTGGAATCTTGGCCCAAGGAAAAAAAATGATTAGGCCACAACCCATGGAACACAAATACTCGTGGAAAAGCTGGGGAAAAGCCAAAATCATAGGAGCAGATGTACAGAACACCACCTTCATCATCGACGGCCCAAACACCCCAGAATGCCCTGATGACCAAAGAGCATGGAACATTTGGGAAGTTGAGGACTATGGATTTGGAATTTTCACGACAAACATATGGTTGAAATTGCGTGACTCCTACACCCAAGTGTGTGACCACCGGCTAATGTCAGCTGCCATCAAGGACAGCAAGGCAGTCCATGCTGACATGGGGTACTGGATAGAAAGTGAAAAGAACGAGACCTGGAAGCTGGCGAGAGCCTCCTTCATAGAAGTTAAGACATGCATCTGGCCAAAATCCCACACTCTATGGAGCAATGGAGTTCTGGAAAGTGAAATGATAATCCCAAAGATATATGGAGGACCAATATCTCAGCACAACTACAGACCAGGATATTTCACACAAACAGCAGGGCCGTGGCACCTAGGCAAGTTGGAACTAGATTTTGATTTGTGTGAAGGTACCACAGTTGTTGTGGATGAACATTGTGGAAATCGAGGACCATCTCTTAGAACCACAACAGTCACAGGAAAGATAATCCATGAATGGTGCTGCAGATCTTGTACGCTACCCCCCTTACGTTTCAAAGGAGAAGACGGGTGTTGGTACGGCATGGAAATCAGACCAGTCAAGGAGAAGGAAGAGAACCTAGTCAAGTCAATGGTCTCTGCAGGGTCAGGAGAAGTGGACAGCTTTTCACTAGGACTGCTATGCATATCAATAATGATTGAAGAGGTGATGAGATCCAGATGGAGTAGAAAAATGCTGATGACTGGAACACTGGCTGTGTTCCTCCTTCTTATAATGGGACAATTGACATGGAATGATCTGATCAGGTTATGCATCATGGTTGGAGCCAATGCTTCAGACAGGATGGGGATGGGAACAACGTACCTAGCTTTGATGGCCACTTTCAAAATGAGACCAATGTTCGCTGTCGGGCTATTATTTCGCAGACTAACATCTAGAGAAGTTCTTCTTCTTACAATTGGATTGAGCCTGGTGGCATCCGTGGAGCTACCAAATTCCTTAGAGGAGCTGGGGGATGGACTTGCAATGGGCATCATGATGTTAAAATTACTGACTGATTTTCAGTCACACCAGCTATGGGCTACCTTGCTGTCCTTGACATTTATCAAAACAACTTTTTCATTGCACTATGCATGGAAGACAATGGCTATGGTACTGTCAATTGTATCTCTCTTCCCTTTATGCCTGTCCACGACCTCTCAAAAAACAACATGGCTTCCGGTGCTGTTGGGATCTCTTGGATGCAAACCACTAACCATGTTTCTTATAACAGAAAACAAAATCTGGGGAAGGAAAAGTTGGCCCCTCAATGAAGGAATTATGGCTGTTGGAATAGTTAGCATTCTACTAAGTTCACTCCTCAAAAATGATGTGCCGCTAGCCGGCCCACTAATAGCTGGAGGCATGCTAATAGCATGTTATGTCATATCCGGAAGCTCAGCCGATTTATCACTGGAGAAAGCGGCTGAGGTCTCCTGGGAAGAAGAAGCAGAACACTCTGGTGCCTCACACAACATACTAGTGGAGGTCCAAGATGATGGAACCATGAAGATAAAAGATGAAGAGAGAGATGACACACTCACCATTCTCCTTAAAGCAACTCTGCTGGCAGTCTCAGGGGTGTACCCAATGTCAATACCAGCGACCCTTTTTGTGTGGTATTTTTGGCAGAAAAAGAAACAGAGATCAGGAGTGCTATGGGACACACCCAGCCCTCCAGAAGTGGAAAGAGCAGTTCTTGATGATGGTATCTATAGAATTTTGCAAAGAGGACTGTTGGGCAGGTCCCAAGTAGGAGTAGGAGTTTTCCAAGAAGGCGTGTTCCACACAATGTGGCACGTCACCAGGGGAGCTGTCCTCATGTATCAAGGGAAGAGGCTGGAACCAAGCTGGGCCAGTGTCAAAAAAGACTTGATCTCATATGGAGGAGGTTGGAGGTTTCAAGGATCCTGGAACACGGGAGAAGAAGTGCAGGTGATTGCTGTTGAACCGGGAAAAAACCCCAAAAATGTACAGACAGCGCCGGGCACCTTCAAGACCCCTGAAGGCGAAGTTGGAGCCATAGCCCTAGATTTTAAACCCGGCACATCTGGATCTCCCATCGTGAACAGAGAGGGAAAAATAGTAGGTCTTTATGGAAATGGAGTGGTGACAACAAGTGGAACCTACGTCAGTGCCATAGCTCAAGCTAAAGCATCACAAGAAGGGCCTCTACCAGAGATTGAGGACGAGGTGTTTAGGAAAAGAAACTTAACAATAATGGACCTACATCCAGGATCGGGAAAAACAAGAAGATATCTTCCAGCCATAGTCCGTGAGGCCATAAAAAGGAAGCTGCGCACGCTAATCTTGGCTCCCACAAGAGTTGTCGCTTCTGAAATGGCAGAGGCGCTCAAGGGAATGCCAATAAGGTATCAGACAACAGCAGTGAAGAGTGAACACACAGGAAAGGAGATAGTTGACCTTATGTGCCACGCCACTTTCACCATGCGTCTCCTGTCTCCCGTGAGAGTTCCCAATTACAACATGATTATCATGGATGAAGCACATTTCACCGATCCAGCCAGCATAGCGGCCAGAGGGTACATCTCAACCCGAGTGGGTATGGGTGAAGCAGCTGCGATCTTTATGACAGCCACTCCCCCAGGATCGGTGGAGGCCTTTCCACAGAGCAATGCAGTTATCCAAGATGAGGAAAGAGACATTCCTGAGAGATCATGGAACTCAGGCTATGACTGGATCACTGATTTCCCAGGTAAAACAGTCTGGTTTGTTCCAAGCATCAAATCAGGAAATGACATTGCCAACTGTTTAAGAAAGAACGGGAAACGGGTGATCCAATTGAGCAGAAAAACCTTTGACACTGAGTACCAGAAAACAAAAAACAACGACTGGGACTATGTCGTCACAACAGACATTTCCGAAATGGGAGCAAACTTCCGGGCCGACAGGGTAATAGACCCAAGGCGGTGTCTGAAACCGGTAATACTAAAAGATGGTCCAGAGCGCGTCATTCTAGCCGGACCGATGCCAGTGACTGTGGCCAGTGCCGCCCAGAGGAGAGGAAGAATTGGAAGGAACCAAAACAAGGAAGGTGATCAGTATATTTACATGGGACAGCCTTTAAACAATGATGAGGACCACGCTCATTGGACAGAAGCAAAAATGCTCCTTGACAATATAAACACACCAGAAGGGATTATCCCAGCCCTCTTTGAGCCGGAGAGAGAAAAGAGTGCAGCAATAGACGGGGAATACAGACTGCGGGGTGAAGCAAGGAAAACGTTCGTGGAGCTCATGAGAAGAGGAGATCTACCTGTCTGGCTATCCTACAAAGTTGCCTCAGAAGGCTTCCAGTACTCCGACAGAAGGTGGTGCTTTGATGGGGAAAGGAACAACCAGGTGTTGGAGGAGAACATGGACGTGGAGATCTGGACAAAAGAAGGAGAAAGAAAGAAACTACGACCCCGCTGGTTGGATGCCAGAACATACTCTGACCCACTGGCTCTGCGCGAGTTTAAAGAGTTTGCAGCAGGAAGAAGAAGCGTCTCAGGTGACCTAATATTAGAAATAGGGAAACTTCCACAACATTTGACGCAAAGGGCCCAGAATGCTTTGGACAACTTGGTCATGTTGCACAATTCCGAACAAGGAGGAAAAGCCTATAGACATGCTATGGAAGAACTACCAGACACCATAGAAACGTTGATGCTCCTAGCTTTGATAGCTGTGTTGACTGGTGGAGTGACGCTGTTCTTCCTATCAGGAAGAGGTCTAGGGAAAACATCCATCGGCCTACTCTGCGTGATGGCCTCAAGCGTACTGTTATGGATGGCCAGTGTGGAGCCCCATTGGATAGCGGCCTCCATCATACTGGAGTTCTTTCTGATGGTGCTGCTTATTCCAGAGCCAGACAGACAGCGCACTCCACAGGACAACCAGCTAGCATATGTGGTGATAGGTTTGTTATTCATGATATTGACAGTGGCAGCCAATGAGATGGGATTATTGGAAACCACAAAGAAAGACCTGGGGATTGGCCATGTAGCTGCTGAAAACCACCACCATGCTACAATGCTGGACGTAGACCTACATCCAGCTTCAGCCTGGACCCTCTATGCAGTGGCCACAACAATTATCACTCCCATGATGAGACACACAATTGAAAACACAACGGCAAATATTTCCCTGACAGCTATTGCAAACCAGGCAGCTATATTGATGGGACTTGACAAGGGATGGCCAATATCGAAGATGGACATAGGAGTTCCACTTCTCGCCTTGGGGTGCTATTCCCAGGTGAACCCGCTGACGCTGACAGCGGCGGTATTGATGCTAGTGGCTCATTACGCCATAATTGGACCTGGACTGCAAGCAAAAGCTACTAGAGAAGCTCAAAAAAGGACAGCGGCCGGAATAATGAAAAATCCAACTGTCGACGGGATTGTTGCAATAGATTTGGATCCTGTGGTTTACGATGCAAAATTTGAAAAACAGCTAGGCCAAATAATGTTGTTGATACTTTGCACATCACAGATTCTCTTGATGCGGACTACATGGGCCTTGTGTGAATCCATCACACTGGCTACTGGACCTCTGACCACTCTTTGGGAGGGATCTCCAGGAAAATTCTGGAACACCACGATAGCGGTGTCCATGGCAAACATTTTCAGGGGAAGTTATCTAGCAGGAGCAGGTCTGGCCTTCTCATTAATGAAATCTCTAGGAGGAGGTAGGAGAGGCACGGGAGCCCAAGGGGAAACACTGGGAGAAAAATGGAAAAGACAGCTAAACCAACTGAGCAAGTCAGAATTCAACACTTACAAAAGGAGTGGGATTATGGAGGTGGATAGATCCGAAGCCAAAGAGGGACTGAAAAGAGGAGAAACAACCAAACATGCAGTGTCGAGAGGAACAGCCAAACTGAGGTGGTTTGTGGAGAGGAACCTTGTGAAACCAGAAGGGAAAGTCATAGACCTCGGTTGTGGAAGAGGTGGCTGGTCATATTATTGCGCTGGGCTGAAGAAAGTCACAGAAGTGAAAGGATACACAAAAGGAGGACCTGGACATGAGGAACCAATCCCAATGGCGACCTATGGATGGAACCTAGTAAAGCTACACTCCGGAAAAGATGTATTCTTTACACCACCTGAGAAATGTGACACCCTTTTGTGTGATATTGGTGAGTCCTCTCCGAACCCAACTATAGAAGAAGGAAGAACGTTACGTGTTCTAAAGATGGTGGAACCATGGCTCAGAGGAAACCAATTTTGCATAAAAATTCTAAATCCCTATATGCCGAGTGTGGTAGAAACTCTGGAGCAAATGCAAAGAAAACATGGAGGAATGCTAGTGCGAAACCCACTCTCAAGAAATTCCACCCATGAAATGTACTGGGTTTCATGTGGAACAGGAAACATTGTGTCAGCAGTAAACATGACATCTAGAATGTTGCTAAATCGATTCACAATGGCTCACAGGAAGCCAACATATGAAAGAGACGTGGACTTAGGCGCTGGAACAAGACATGTGGCAGTGGAACCAGAGGTAGCCAACCTAGATATCATTGGCCAGAGGATAGAGAATATAAAAAATGAACATAAGTCAACATGGCATTATGATGAGGACAATCCATACAAAACATGGGCCTATCATGGATCATATGAGGTCAAGCCATCAGGATCAGCCTCATCCATGGTCAATGGCGTGGTGAGATTGCTCACCAAACCATGGGATGTTATCCCCATGGTCACACAAATAGCCATGACTGACACCACACCCTTTGGACAACAGAGGGTGTTTAAAGAGAAAGTTGACACGCGCACACCAAAAGCAAAACGAGGCACAGCACAAATTATGGAGGTGACAGCCAGGTGGTTATGGGGTTTCCTTTCTAGAAACAAAAAACCCAGAATCTGCACAAGAGAGGAGTTCACAAGAAAAGTTAGGTCAAACGCAGCTATTGGAGCAGTGTTCGTTGATGAAAATCAATGGAACTCAGCAAAAGAAGCAGTGGAAGACGAACGGTTCTGGGACCTTGTGCACAGAGAGAGGGAGCTTCATAAACAGGGAAAATGTGCCACGTGTGTCTACAATATGATGGGGAAGAGAGAGAAAAAATTAGGAGAGTTCGGAAAGGCAAAAGGAAGTCGTGCAATATGGTACATGTGGTTGGGAGCACGCTTTCTAGAGTTCGAAGCCCTTGGTTTCATGAATGAAGATCACTGGTTCAGTAGAGAGAATTCACTCAGTGGAGTGGAAGGAGAAGGACTCCACAAACTTGGATACATACTCAGAGACATATCAAAGATTCCAGGGGGAAATATGTATGCAGATGACACAGCCGGATGGGACACAAGAATAACAGAGGATGATCTTCAGAATGAGGCTAAAATCACTGACATCATGGAGCCCGAACATGCCCTATTGGCTACGTCAATCTTTAAGCTGACCTACCAAAATAAGGTGGTAAGGGTGCAGAGACCAGCAAAAAATGGAACCGTGATGGATGTTATATCCAGACGTGACCAGAGAGGAAGTGGACAGGTCGGAACTTATGGCTTAAACACTTTCACCAACATGGAGGCCCAACTAATAAGACAAATGGAGTCTGAGGGAATCTTTTTACCCAGCGAATTGGAAACCCCAAATCTAGCCGAAAGAGTTCTCGACTGGTTGGAAAAACATGGCGTCGAAAGGCTGAAAAGAATGGCAATCAGCGGAGATGACTGTGTGGTGAAACCAATTGATGACAGGTTCGCAACAGCCTTAACAGCTTTGAATGACATGGGAAAAGTAAGAAAAGACATACCGCAATGGGAACCTTCAAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGTTCACACCATTTCCACCAGCTGATTATGAAGGATGGGAGGGAGATAGTGGTGCCATGCCGCAACCAAGATGAACTTGTGGGTAGGGCCAGAGTATCACAAGGCGCCGGATGGAGCCTGAGAGAAACTGCATGCCTAGGCAAGTCATATGCACAAATGTGGCAGCTGATGTACTTCCACAGGAGAGACCTGAGACTAGCGGCTAATGCTATCTGTTCAGCCGTTCCAGTTGATTGGGTCCCAACCAGCCGCACCACCTGGTCGATCCATGCCCATCACCAATGGATGACAACAGAAGACATGTTATCAGTGTGGAATAGGGTTTGGATAGAGGAAAACCCATGGATGGAGGATAAAACTCATGTATCCAGTTGGGAAGATGTTCCATACTTAGGAAAAAGGGAAGATCAGTGGTGTGGATCCCTGATAGGCTTAACAGCAAGGGCCACCTGGGCCACTAACATACAAGTGGCCATAAACCAAGTGAGAAGGCTCATTGGGAATGAGAATTATCTAGATTACATGACATCAATGAAGAGATTCAAGAATGAGAGTGATCCCGAAGGGGCACTCTGGTAAGTCAACACATTCACAAAATAAAGGAAAATAAAAAATCAAACAAGGCAAGAAGTCAGGCCGGATTAAGCCATAGTACGGTAAGAGCTATGCTGCCTGTGAGCCCCGTCCAAGGACGTAAAATGAAGTCAGGCCGAAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTGGCTCCATCGTGGGGATGTAAAAACCCGGGAGGCTGCAACCCATGGAAGCTGTACGCATGGGGTAGCAGACTAGTGGTTAGAGGAGACCCCTCCCAAGACACAACGCAGCAGCGGGGCCCAACACCAGGGGAAGCTGTACCCTGGTGGTAAGGACTAGAGGTTAGAGGAGACCCCCCGCACAACAATAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCTACAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT", "2K": "TPQDNQLAYVVIGLLFMILTVAA", "C": "MNNQRKKTGRPSFNMLKRARNRVSTVSQLAKRFSKGLLSGQGPMKLVMAFIAFLRFLAIPPTAGILARWGSFKKNGAIKVLRGFKKEISNMLNIMNRRKRSVTMLLMLLPTALA", "E": "MRCVGIGNRDFVEGLSGATWVDVVLEHGSCVTTMAKNKPTLDIELLKTEVTNPAVLRKLCIEAKISNTTTDSRCPTQGEATLVEEQDANFVCRRTFVDRGWGNGCGLFGKGSLITCAKFKCVTKLEGKIVQYENLKYSVIVTVHTGDQHQVGNETTEHGTTATITPQAPTSEIQLTDYGALTLDCSPRTGLDFNEMVLLTMKEKSWLVHKQWFLDLPLPWTSGASTSQETWNRQDLLVTFKTAHAKKQEVVVLGSQEGAMHTALTGATEIQTSGTTTIFAGHLKCRLKMDKLTLKGMSYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSTQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKGSSIGKMFEATARGARRMAILGDTAWDFGSIGGVFTSVGKLVHQVFGTAYGVLFSGVSWTMKIGIGILLTWLGLNSRSTSLSMTCIAVGMVTLYLGVMVQA", "M": "FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMTYKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVGLGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQKGIIFILLMLVTPSMA", "NS1": "DSGCVINWKGRELKCGSGIFVTNEVHTWTEQYKFQADSPKRLSAAIGKAWEEGVCGIRSATRLENIMWKQISNELNHILLENDMKFTVVVGDVSGILAQGKKMIRPQPMEHKYSWKSWGKAKIIGADVQNTTFIIDGPNTPECPDDQRAWNIWEVEDYGFGIFTTNIWLKLRDSYTQVCDHRLMSAAIKDSKAVHADMGYWIESEKNETWKLARASFIEVKTCIWPKSHTLWSNGVLESEMIIPKIYGGPISQHNYRPGYFTQTAGPWHLGKLELDFDLCEGTTVVVDEHCGNRGPSLRTTTVTGKIIHEWCCRSCTLPPLRFKGEDGCWYGMEIRPVKEKEENLVKSMVSA", "NS2A": "GSGEVDSFSLGLLCISIMIEEVMRSRWSRKMLMTGTLAVFLLLIMGQLTWNDLIRLCIMVGANASDRMGMGTTYLALMATFKMRPMFAVGLLFRRLTSREVLLLTIGLSLVASVELPNSLEELGDGLAMGIMMLKLLTDFQSHQLWATLLSLTFIKTTFSLHYAWKTMAMVLSIVSLFPLCLSTTSQKTTWLPVLLGSLGCKPLTMFLITENKIWGRK", "NS2B": "SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSADLSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLKATLLAVSGVYPMSIPATLFVWYFWQKKKQR", "NS3": "SGVLWDTPSPPEVERAVLDDGIYRILQRGLLGRSQVGVGVFQEGVFHTMWHVTRGAVLMYQGKRLEPSWASVKKDLISYGGGWRFQGSWNTGEEVQVIAVEPGKNPKNVQTAPGTFKTPEGEVGAIALDFKPGTSGSPIVNREGKIVGLYGNGVVTTSGTYVSAIAQAKASQEGPLPEIEDEVFRKRNLTIMDLHPGSGKTRRYLPAIVREAIKRKLRTLILAPTRVVASEMAEALKGMPIRYQTTAVKSEHTGKEIVDLMCHATFTMRLLSPVRVPNYNMIIMDEAHFTDPASIAARGYISTRVGMGEAAAIFMTATPPGSVEAFPQSNAVIQDEERDIPERSWNSGYDWITDFPGKTVWFVPSIKSGNDIANCLRKNGKRVIQLSRKTFDTEYQKTKNNDWDYVVTTDISEMGANFRADRVIDPRRCLKPVILKDGPERVILAGPMPVTVASAAQRRGRIGRNQNKEGDQYIYMGQPLNNDEDHAHWTEAKMLLDNINTPEGIIPALFEPEREKSAAIDGEYRLRGEARKTFVELMRRGDLPVWLSYKVASEGFQYSDRRWCFDGERNNQVLEENMDVEIWTKEGERKKLRPRWLDARTYSDPLALREFKEFAAGRR", "NS4A": "SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPDTIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASVEPHWIAASIILEFFLMVLLIPEPDRQR", "NS4B": "NEMGLLETTKKDLGIGHVAAENHHHATMLDVDLHPASAWTLYAVATTIITPMMRHTIENTTANISLTAIANQAAILMGLDKGWPISKMDIGVPLLALGCYSQVNPLTLTAAVLMLVAHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGIVAIDLDPVVYDAKFEKQLGQIMLLILCTSQILLMRTTWALCESITLATGPLTTLWEGSPGKFWNTTIAVSMANIFRGSYLAGAGLAFSLMKSLGGGRR", "NS5": "GTGAQGETLGEKWKRQLNQLSKSEFNTYKRSGIMEVDRSEAKEGLKRGETTKHAVSRGTAKLRWFVERNLVKPEGKVIDLGCGRGGWSYYCAGLKKVTEVKGYTKGGPGHEEPIPMATYGWNLVKLHSGKDVFFTPPEKCDTLLCDIGESSPNPTIEEGRTLRVLKMVEPWLRGNQFCIKILNPYMPSVVETLEQMQRKHGGMLVRNPLSRNSTHEMYWVSCGTGNIVSAVNMTSRMLLNRFTMAHRKPTYERDVDLGAGTRHVAVEPEVANLDIIGQRIENIKNEHKSTWHYDEDNPYKTWAYHGSYEVKPSGSASSMVNGVVRLLTKPWDVIPMVTQIAMTDTTPFGQQRVFKEKVDTRTPKAKRGTAQIMEVTARWLWGFLSRNKKPRICTREEFTRKVRSNAAIGAVFVDENQWNSAKEAVEDERFWDLVHRERELHKQGKCATCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGFMNEDHWFSRENSLSGVEGEGLHKLGYILRDISKIPGGNMYADDTAGWDTRITEDDLQNEAKITDIMEPEHALLATSIFKLTYQNKVVRVQRPAKNGTVMDVISRRDQRGSGQVGTYGLNTFTNMEAQLIRQMESEGIFLPSELETPNLAERVLDWLEKHGVERLKRMAISGDDCVVKPIDDRFATALTALNDMGKVRKDIPQWEPSKGWNDWQQVPFCSHHFHQLIMKDGREIVVPCRNQDELVGRARVSQGAGWSLRETACLGKSYAQMWQLMYFHRRDLRLAANAICSAVPVDWVPTSRTTWSIHAHHQWMTTEDMLSVWNRVWIEENPWMEDKTHVSSWEDVPYLGKREDQWCGSLIGLTARATWATNIQVAINQVRRLIGNENYLDYMTSMKRFKNESDPEGALW", "pr": "FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMTYKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKR"}} \ No newline at end of file diff --git a/nextclade/datasets/denv2/genome_annotation.gff3 b/nextclade/datasets/denv2/genome_annotation.gff3 index 1f350fbc..40026b43 100644 --- a/nextclade/datasets/denv2/genome_annotation.gff3 +++ b/nextclade/datasets/denv2/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_001474.2 1 10723 -NC_001474.2 feature gene 97 438 . + . codon_start=1;gene=C;gene_name=C; -NC_001474.2 feature gene 439 711 . + . codon_start=1;gene=pr;gene_name=pr; -NC_001474.2 feature gene 439 936 . + . codon_start=1;gene=M;gene_name=M; -NC_001474.2 feature gene 937 2421 . + . codon_start=1;gene=E;gene_name=E; -NC_001474.2 feature gene 2422 3477 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_001474.2 feature gene 3478 4131 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_001474.2 feature gene 4132 4521 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_001474.2 feature gene 4522 6375 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_001474.2 feature gene 6376 6756 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_001474.2 feature gene 6757 6825 . + . codon_start=1;gene=2K;gene_name=2K; -NC_001474.2 feature gene 6826 7569 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_001474.2 feature gene 7570 10269 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome 1 10723 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 97 438 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 439 711 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 439 936 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 937 2421 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 2422 3477 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 3478 4131 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 4132 4521 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 4522 6375 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 6376 6756 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 6757 6825 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 6826 7569 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 7570 10269 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/datasets/denv2/pathogen.json b/nextclade/datasets/denv2/pathogen.json index b968b789..a1cac1fd 100644 --- a/nextclade/datasets/denv2/pathogen.json +++ b/nextclade/datasets/denv2/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/datasets/denv2/reference.fasta b/nextclade/datasets/denv2/reference.fasta index 1610f7c4..271ec64d 100644 --- a/nextclade/datasets/denv2/reference.fasta +++ b/nextclade/datasets/denv2/reference.fasta @@ -1,180 +1,2 @@ ->NC_001474.2 Dengue virus 2, complete genome -AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAACGTA -GTTCTAACAGTTTTTTAATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCG -AAAAACACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAG -CTGACAAAGAGATTCTCACTTGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATG -GCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATATTGAAGAGA -TGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAGGAAAGAGATT -GGAAGGATGCTGAACATCTTGAATAGGAGACGCAGATCTGCAGGCATGATCATTATGCTG -ATTCCAACAGTGATGGCGTTCCATTTAACCACACGTAACGGAGAACCACACATGATCGTC -AGCAGACAAGAGAAAGGGAAAAGTCTTCTGTTTAAAACAGAGGATGGCGTGAACATGTGT -ACCCTCATGGCCATGGACCTTGGTGAATTGTGTGAAGACACAATCACGTACAAGTGTCCC -CTTCTCAGGCAGAATGAGCCAGAAGACATAGACTGTTGGTGCAACTCTACGTCCACGTGG -GTAACTTATGGGACGTGTACCACCATGGGAGAACATAGAAGAGAAAAAAGATCAGTGGCA -CTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAA -GGGGCCTGGAAACATGTCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTCACC -ATGATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATT -TTCATCTTACTGACAGCTGTCACTCCTTCAATGACAATGCGTTGCATAGGAATGTCAAAT -AGAGACTTTGTGGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGA -AGCTGTGTGACGACGATGGCAAAAAACAAACCAACATTGGATTTTGAACTGATAAAAACA -GAAGCCAAACAGCCTGCCACCCTAAGGAAGTACTGTATAGAGGCAAAGCTAACCAACACA -ACAACAGAATCTCGCTGCCCAACACAAGGGGAACCCAGCCTAAATGAAGAGCAGGACAAA -AGGTTCGTCTGCAAACACTCCATGGTAGACAGAGGATGGGGAAATGGATGTGGACTATTT -GGAAAGGGAGGCATTGTGACCTGTGCTATGTTCAGATGCAAAAAGAACATGGAAGGAAAA -GTTGTGCAACCAGAAAACTTGGAATACACCATTGTGATAACACCTCACTCAGGGGAAGAG -CATGCAGTCGGAAATGACACAGGAAAACATGGCAAGGAAATCAAAATAACACCACAGAGT -TCCATCACAGAAGCAGAATTGACAGGTTATGGCACTGTCACAATGGAGTGCTCTCCAAGA -ACGGGCCTCGACTTCAATGAGATGGTGTTGCTGCAGATGGAAAATAAAGCTTGGCTGGTG -CACAGGCAATGGTTCCTAGACCTGCCGTTACCATGGTTGCCCGGAGCGGACACACAAGGG -TCAAATTGGATACAGAAAGAGACATTGGTCACTTTCAAAAATCCCCATGCGAAGAAACAG -GATGTTGTTGTTTTAGGATCCCAAGAAGGGGCCATGCACACAGCACTTACAGGGGCCACA -GAAATCCAAATGTCATCAGGAAACTTACTCTTCACAGGACATCTCAAGTGCAGGCTGAGA -ATGGACAAGCTACAGCTCAAAGGAATGTCATACTCTATGTGCACAGGAAAGTTTAAAGTT -GTGAAGGAAATAGCAGAAACACAACATGGAACAATAGTTATCAGAGTGCAATATGAAGGG -GACGGCTCTCCATGCAAGATCCCTTTTGAGATAATGGATTTGGAAAAAAGACATGTCTTA -GGTCGCCTGATTACAGTCAACCCAATTGTGACAGAAAAAGATAGCCCAGTCAACATAGAA -GCAGAACCTCCATTCGGAGACAGCTACATCATCATAGGAGTAGAGCCGGGACAACTGAAG -CTCAACTGGTTTAAGAAAGGAAGTTCTATCGGCCAAATGTTTGAGACAACAATGAGGGGG -GCGAAGAGAATGGCCATTTTAGGTGACACAGCCTGGGATTTTGGATCCTTGGGAGGAGTG -TTTACATCTATAGGAAAGGCTCTCCACCAAGTCTTTGGAGCAATCTATGGAGCTGCCTTC -AGTGGGGTTTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATG -AATTCACGCAGCACCTCACTGTCTGTGACACTAGTATTGGTGGGAATTGTGACACTGTAT -TTGGGAGTCATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTG -AAATGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGGACAGAACAATACAAG -TTCCAACCAGAATCCCCTTCAAAACTAGCTTCAGCTATCCAGAAAGCCCATGAAGAGGGC -ATTTGTGGAATCCGCTCAGTAACAAGACTGGAGAATCTGATGTGGAAACAAATAACACCA -GAATTGAATCACATTCTATCAGAAAATGAGGTGAAGTTAACTATTATGACAGGAGACATC -AAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCTCAGCCCACTGAGCTGAAGTAT -TCATGGAAAACATGGGGCAAAGCAAAAATGCTCTCTACAGAGTCTCATAACCAGACCTTT -CTCATTGATGGCCCCGAAACAGCAGAATGCCCCAACACAAATAGAGCTTGGAATTCGTTG -GAAGTTGAAGACTATGGCTTTGGAGTATTCACCACCAATATATGGCTAAAATTGAAAGAA -AAACAGGATGTATTCTGCGACTCAAAACTCATGTCAGCGGCCATAAAAGACAACAGAGCC -GTCCATGCCGATATGGGTTATTGGATAGAAAGTGCACTCAATGACACATGGAAGATAGAG -AAAGCCTCTTTCATTGAAGTTAAAAACTGCCACTGGCCAAAATCACACACCCTCTGGAGC -AATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATCTCGCTGGACCAGTGTCTCAA -CACAACTATAGACCAGGCTACCATACACAAATAACAGGACCATGGCATCTAGGTAAGCTT -GAGATGGACTTTGATTTCTGTGATGGAACAACAGTGGTAGTGACTGAGGACTGCGGAAAT -AGAGGACCCTCTTTGAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGC -CGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGGTGCTGGTACGGGATG -GAAATCAGACCATTGAAGGAGAAAGAAGAGAATTTGGTCAACTCCTTGGTCACAGCTGGA -CATGGGCAGGTCGACAACTTTTCACTAGGAGTCTTGGGAATGGCATTGTTCCTGGAGGAA -ATGCTTAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTTGTG -ACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTAGGC -GCCACTATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCCTACTAGCAGCCTTC -AAAGTCAGACCAACTTTTGCAGCTGGACTACTCTTGAGAAAGCTGACCTCCAAGGAATTG -ATGATGACTACTATAGGAATTGTACTCCTCTCCCAGAGCACCATACCAGAGACCATTCTT -GAGTTGACTGATGCGTTAGCCTTAGGCATGATGGTCCTCAAAATGGTGAGAAATATGGAA -AAGTATCAATTGGCAGTGACTATCATGGCTATCTTGTGCGTCCCAAACGCAGTGATATTA -CAAAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCCGTTTCCCCACTGCTC -TTAACATCCTCACAGCAAAAAACAGATTGGATACCATTAGCATTGACGATCAAAGGTCTC -AATCCAACAGCTATTTTTCTAACAACCCTCTCAAGAACCAGCAAGAAAAGGAGCTGGCCA -TTAAATGAGGCTATCATGGCAGTCGGGATGGTGAGCATTTTAGCCAGTTCTCTCCTAAAA -AATGATATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTG -CTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCAGCCGATGTCAAATGGGAAGAC -CAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGC -ATGTCGATAAAAAATGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTG -CTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTG -TGGGAAGTGAAGAAACAACGGGCCGGAGTATTGTGGGATGTTCCTTCACCCCCACCCATG -GGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATTAAGCAAAAAGGGATTCTTGGATAT -TCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCATACAATGTGGCATGTCACA -CGTGGCGCTGTTCTAATGCATAAAGGAAAGAGGATTGAACCATCATGGGCGGACGTCAAG -AAAGACCTAATATCATATGGAGGAGGCTGGAAGTTAGAAGGAGAATGGAAGGAAGGAGAA -GAAGTCCAGGTATTGGCACTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACGAAACCT -GGTCTTTTCAAAACCAACGCCGGAACAATAGGTGCTGTATCTCTGGACTTTTCTCCTGGA -ACGTCAGGATCTCCAATTATCGACAAAAAAGGAAAAGTTGTGGGTCTTTATGGTAATGGT -GTTGTTACAAGGAGTGGAGCATATGTGAGTGCTATAGCCCAGACTGAAAAAAGCATTGAA -GACAACCCAGAGATCGAAGATGACATTTTCCGAAAGAGAAGACTGACCATCATGGACCTC -CACCCAGGAGCGGGAAAGACGAAGAGATACCTTCCGGCCATAGTCAGAGAAGCTATAAAA -CGGGGTTTGAGAACATTAATCTTGGCCCCCACTAGAGTTGTGGCAGCTGAAATGGAGGAA -GCCCTTAGAGGACTTCCAATAAGATACCAGACCCCAGCCATCAGAGCTGAGCACACCGGG -CGGGAGATTGTGGACCTAATGTGTCATGCCACATTTACCATGAGGCTGCTATCACCAGTT -AGAGTGCCAAACTACAACCTGATTATCATGGACGAAGCCCATTTCACAGACCCAGCAAGT -ATAGCAGCTAGAGGATACATCTCAACTCGAGTGGAGATGGGTGAGGCAGCTGGGATTTTT -ATGACAGCCACTCCCCCGGGAAGCAGAGACCCATTTCCTCAGAGCAATGCACCAATCATA -GATGAAGAAAGAGAAATCCCTGAACGTTCGTGGAATTCCGGACATGAATGGGTCACGGAT -TTTAAAGGGAAGACTGTTTGGTTCGTTCCAAGTATAAAAGCAGGAAATGATATAGCAGCT -TGCCTGAGGAAAAATGGAAAGAAAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAG -TATGTCAAGACTAGAACCAATGATTGGGACTTCGTGGTTACAACTGACATTTCAGAAATG -GGTGCCAATTTCAAGGCTGAGAGGGTTATAGACCCCAGACGCTGCATGAAACCAGTCATA -CTAACAGATGGTGAAGAGCGGGTGATTCTGGCAGGACCTATGCCAGTGACCCACTCTAGT -GCAGCACAAAGAAGAGGGAGAATAGGAAGAAATCCAAAAAATGAGAATGACCAGTACATA -TACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAAGAAGCTAAAATG -CTCCTAGATAACATCAACACGCCAGAAGGAATCATTCCTAGCATGTTCGAACCAGAGCGT -GAAAAGGTGGATGCCATTGATGGCGAATACCGCTTGAGAGGAGAAGCAAGGAAAACCTTT -GTAGACTTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCCTACAGAGTGGCAGCTGAA -GGCATCAACTACGCAGACAGAAGGTGGTGTTTTGATGGAGTCAAGAACAACCAAATCCTA -GAAGAAAACGTGGAAGTTGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTGAAACCC -AGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTTAAGGAATTT -GCAGCCGGAAGAAAGTCTCTGACCCTGAACCTAATCACAGAAATGGGTAGGCTCCCAACC -TTCATGACTCAGAAGGCAAGAGACGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAG -GCAGGTGGAAGGGCGTACAACCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTG -CTTTTACTGACACTTCTGGCTACAGTCACGGGAGGGATCTTTTTATTCTTGATGAGCGGA -AGGGGCATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCTAGCATCCTCCTA -TGGTACGCACAAATACAGCCACACTGGATAGCAGCTTCAATAATACTGGAGTTTTTTCTC -ATAGTTTTGCTTATTCCAGAACCTGAAAAACAGAGAACACCCCAAGACAACCAACTGACC -TACGTTGTCATAGCCATCCTCACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTC -CTAGAAAAAACGAAGAAAGATCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGC -AACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACA -ACATTTGTTACACCAATGTTGAGACATAGCATTGAAAATTCCTCAGTGAATGTGTCCCTA -ACAGCTATAGCCAACCAAGCCACAGTGTTAATGGGTCTCGGGAAAGGATGGCCATTGTCA -AAGATGGACATCGGAGTTCCCCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATA -ACTCTCACAGCAGCTCTTTTCTTATTGGTAGCACATTATGCCATCATAGGGCCAGGACTC -CAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGCAGCGGCGGGCATCATGAAAAACCCA -ACTGTCGATGGAATAACAGTGATTGACCTAGATCCAATACCTTATGATCCAAAGTTTGAA -AAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTATTGATGATGAGG -ACTACATGGGCTCTGTGTGAGGCTTTAACCTTAGCTACCGGGCCCATCTCCACATTGTGG -GAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCGGTGTCAATGGCTAACATTTTT -AGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCTATTATGAAGAACACAACCAAC -ACAAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAATGGAAAAGCCGATTG -AACGCATTGGGAAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGAT -AGAACCTTAGCAAAAGAAGGCATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGA -GGCTCAGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCACACCAGAAGGGAAAGTA -GTGGACCTCGGTTGTGGCAGAGGAGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTA -AGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAACCCATCCCCATGTCA -ACATATGGGTGGAATCTAGTGCGTCTTCAAAGTGGAGTTGACGTTTTCTTCATCCCGCCA -GAAAAGTGTGACACATTATTGTGTGACATAGGGGAGTCATCACCAAATCCCACAGTGGAA -GCAGGACGAACACTCAGAGTCCTTAACTTAGTAGAAAATTGGTTGAACAACAACACTCAA -TTTTGCATAAAGGTTCTCAACCCATATATGCCCTCAGTCATAGAAAAAATGGAAGCACTA -CAAAGGAAATATGGAGGAGCCTTAGTGAGGAATCCACTCTCACGAAACTCCACACATGAG -ATGTACTGGGTATCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGG -ATGTTGATCAACAGATTTACAATGAGATACAAGAAAGCCACTTACGAGCCGGATGTTGAC -CTCGGAAGCGGAACCCGTAACATCGGGATTGAAAGTGAGATACCAAACCTAGATATAATT -GGGAAAAGAATAGAAAAAATAAAGCAAGAGCATGAAACATCATGGCACTATGACCAAGAC -CACCCATACAAAACGTGGGCATACCATGGTAGCTATGAAACAAAACAGACTGGATCAGCA -TCATCCATGGTCAACGGAGTGGTCAGGCTGCTGACAAAACCTTGGGACGTCGTCCCCATG -GTGACACAGATGGCAATGACAGACACGACTCCATTTGGACAACAGCGCGTTTTTAAAGAG -AAAGTGGACACGAGAACCCAAGAACCGAAAGAAGGCACGAAGAAACTAATGAAAATAACA -GCAGAGTGGCTTTGGAAAGAATTAGGGAAGAAAAAGACACCCAGGATGTGCACCAGAGAA -GAATTCACAAGAAAGGTGAGAAGCAATGCAGCCTTGGGGGCCATATTCACTGATGAGAAC -AAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATAGTAGGTTTTGGGAGCTGGTTGACAAG -GAAAGGAATCTCCATCTTGAAGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAA -AGAGAGAAGAAGCTAGGGGAATTCGGCAAGGCAAAAGGCAGCAGAGCCATATGGTACATG -TGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTAAATGAAGATCACTGG -TTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGCACAAGCTAGGTTAC -ATTCTAAGAGACGTGAGCAAGAAAGAGGGAGGAGCAATGTATGCCGATGACACCGCAGGA -TGGGATACAAGAATCACACTAGAAGACCTAAAAAATGAAGAAATGGTAACAAACCACATG -GAAGGAGAACACAAGAAACTAGCCGAGGCCATTTTCAAACTAACGTACCAAAACAAGGTG -GTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGACATCATATCGAGAAGAGAC -CAAAGAGGTAGTGGACAAGTTGGCACCTATGGACTCAATACTTTCACCAATATGGAAGCC -CAACTAATCAGACAGATGGAGGGAGAAGGAGTCTTTAAAAGCATTCAGCACCTAACAATC -ACAGAAGAAATCGCTGTGCAAAACTGGTTAGCAAGAGTGGGGCGCGAAAGGTTATCAAGA -ATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTTTAGATGACAGGTTCGCAAGCGCT -TTAACAGCTCTAAATGACATGGGAAAGATTAGGAAAGACATACAACAATGGGAACCTTCA -AGAGGATGGAATGATTGGACACAAGTGCCCTTCTGTTCACACCATTTCCATGAGTTAATC -ATGAAAGACGGTCGCGTACTCGTTGTTCCATGTAGAAACCAAGATGAACTGATTGGCAGA -GCCCGAATCTCCCAAGGAGCAGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCT -TACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGCGACCTCAGGCTGGCGGCAAAT -GCTATTTGCTCGGCAGTACCATCACATTGGGTTCCAACAAGTCGAACAACCTGGTCCATA -CATGCTAAACATGAATGGATGACAACGGAAGACATGCTGACAGTCTGGAACAGGGTGTGG -ATTCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCA -TACTTGGGGAAAAGAGAAGACCAATGGTGCGGCTCATTGATTGGGTTAACAAGCAGGGCC -ACCTGGGCAAAGAACATCCAAGCAGCAATAAATCAAGTTAGATCCCTTATAGGCAATGAA -GAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAAGCAGGA -GTTCTGTGGTAGAAAGCAAAACTAACATGAAACAAGGCTAGAAGTCAGGTCGGATTAAGC -CATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCA -GGCCATCATAAATGCCATAGCTTGAGTAAACTATGCAGCCTGTAGCTCCACCTGAGAAGG -TGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGC -GGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGCGAGATGA -AGCTGTAGTCTCGCTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCGAAACAAAAAACAG -CATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACA -GAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome +AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAACGTAGTTCTAACAGTTTTTTGATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCGAGAAATACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTACAACAGCTGACAAAGAGATTCTCACTTGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATACTGAAAAGATGGGGAACAATCAAAAAATCAAAGGCTATCAATGTCCTGAGAGGGTTCAGGAAAGAGATTGGAAGGATGCTGAACATCTTGAACAGGAGACGCAGAACTGCAGGCATGATCATCATGCTGATTCCAACAGTGATGGCGTTCCATTTGACCACACGCAACGGAGAACCACACATGATTGTCAGTAGACAAGAGAAAGGGAAAAGCCTTCTGTTTAAAACAGAGGATGGTATGAACATGTGTACCCTCATGGCCATGGACCTTGGTGAGTTGTGTGAAGACACAATCACGTACAAGTGTCCTTTTCTCAGGCAGAACGAACCAGAAGACATAGATTGTTGGTGCAACTCCACGTCCACATGGGTAACTTATGGGACATGTACCACCACAGGAGAGCACAGAAGAGAAAAAAGATCAGTGGCACTTGTTCCACACGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGCCCAGAGAATTGAAACTTGGATTCTGAGACATCCAGGCTTTACCATAATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGTCCTGATTTTCATCTTACTGACAGCCGTCGCTCCTTCAATGACAATGCGCTGCATAGGAATATCAAATAGAGACTTTGTGGAAGGAGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGAAGCTGTGTGACGACGATGGCAAAAAACAAACCAACATTGGACTTTGAACTGATAAAAACAGAAGCCAAACAACCTGCCACTCTAAGGAAGTACTGTATAGAGGCTAAACTGACCAACACAACAACAGAATCTCGCTGCCCAACACAAGGGGAACCCAGCCTAAATGAAGAGCAGGACAAAAGGTTCGTCTGCAAACACTCCATGGTAGACAGAGGATGGGGAAATGGATGTGGATTATTTGGAAAAGGAGGCATTGTGACCTGTGCTATGTTCACATGCAAAAAGAACATGGAAGGAAAAGTTGTGCAGCCAGAAAACTTGGAATACACCATTGTGATAACACCTCACTCAGGGGAAGAACATGCAGTCGGAAATGACACAGGAAAACATGGCAAGGAAGTCAAGATAACACCACAGAGCTCCATCACAGAAGCAGAACTGACAGGCTATGGCACTGTCACGATGGAGTGCTCTCCGAGAACGGGCCTCGACTTCAATGAGATGGTGTTGCTGCAAATGGAAAACAAAGCTTGGCTGGTGCACAGACAATGGTTCCTAGACCTACCGTTACCATGGCTGCCCGGAGCAGACACACAAGGATCAAATTGGATACAGAAAGAGACATTGGTCACTTTCAAAAATCCCCATGCGAAAAAACAGGATGTTGTTGTCTTAGGATCCCAAGAGGGGGCCATGCACACAGCACTCACAGGGGCCACAGAAATCCAGATGTCATCAGGAAACTTACTGTTCACAGGACATCTCAAGTGCAGGCTGAGAATGGACAAACTACAGCTCAAAGGGATGTCATACTCTATGTGCACAGGAAAGTTTAAAGTTGTGAAGGAAATAGCAGAAACACAACATGGAACAATAGTCATCAGAGTACAATATGAAGGAGACGGCTCTCCATGCAAGATCCCTTTTGAGATAATGGATTTGGAAAAAAGACATGTCTTAGGTCGCCTGATCACAGTCAACCCAATTGTAACAGAAAAAGACAGCCCAGTCAACATAGAAGCAGAACCTCCATTCGGAGACAGCTACATCATCATAGGAGTGGAACCAGGACAATTGAAGCTCAACTGGTTTAAGAAAGGAAGTTCTATCGGCCAAATGTTTGAGACAACAATGAGAGGAGCGAAAAGAATGGCCATTTTGGGTGACACAGCCTGGGATTTTGGATCCCTGGGAGGAGTGTTCACATCTATAGGAAAGGCTCTCCACCAAGTTTTTGGAGCAATCTATGGGGCTGCCTTCAGTGGGGTCTCATGGACTATGAAGATCCTCATAGGAGTTATCATCACATGGATAGGAATGAATTCACGCAGCACCTCACTGTCTGTGTCACTAGTATTAGTGGGAATCGTGACACTATACTTGGGAGTTATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAGAACAAAGAACTGAAATGTGGCAGTGGGATTTTCGTCACAGACAACGTGCACACATGGACAGAACAATACAAGTTCCAACCAGAATCCCCTTCAAAACTGGCTTCAGCCATCCAGAAAGCTCATGAAGAGGGCATTTGTGGAATCCGCTCAGTAACAAGACTGGAGAATCTGATGTGGAAACAGATAACACCAGAATTGAATCACATTCTATCAGAAAATGAAGTAAAGCTGACCATCATGACAGGAGACATTAAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCCCAACCCACTGAGCTGAGGTATTCATGGAAAACATGGGGCAAAGCGAAAATGCTCTCCACAGAGCTCCATAATCAGACCTTTCTCATTGATGGTCCCGAAACAGCAGAATGCCCCAACACAAACAGAGCTTGGAATTCACTGGAAGTTGAGGACTATGGCTTTGGAGTATTCACCACCAATATATGGCTAAAATTGAGAGAAAAGCAGGATGTATTTTGTGACTCAAAACTCATGTCAGCGGCCATAAAGGACAACAGAGCCGTCCATGCTGATATGGGTTATTGGATAGAAAGCGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAGCTGCCACTGGCCAAAGTCACACACCCTCTGGAGTAATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATTTCGCTGGACCAGTGTCACAACACAACTACAGACCAGGCTATTACACACAAACAGCAGGACCTTGGCATCTAGGCAAGCTTGAGATGGACTTTGATTTCTGCGAAGGAACTACAGTGGTGGTGACCGAGGACTGTGGAAACAGAGGACCCTCTTTAAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGCCGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGATGCTGGTACGGGATGGAAATCAGACCATTGAAAGAGAAAGAAGAGAATCTGGTCAACTCTTTGGTCACAGCCGGACATGGGCAGATTGACAACTTTTCACTAGGAATCTTGGGAATGGCATTGTTCCTGGAAGAAATGCTCAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTCGTGACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTGGGCGCTACCATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCCTACTAGCAGCTTTCAAAGTCAGACCAACCTTTGCAGCTGGACTGCTCTTGAGAAAACTGACCTCCAAGGAATTGATGATGACCACCATAGGAATCGTTCTCCTCTCCCAGAGTAGCATACCAGAGACCATTCTTGAACTGACTGATGCGTTAGCCTTGGGCATGATGGTCCTCAAAATAGTGAGAAACATGGAAAAATATCAGCTGGCAGTGACCATCATGGCTATCTTATGCGTCCCAAATGCTGTGATATTACAGAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCTGTTTCCCCACTGCTCTTAACATCCTCACAACAGAAAGCGGATTGGATACCATTAGCATTGACGATCAAAGGTCTCAATCCAACAGCCATTTTTCTAACAACCCTTTCAAGAACCAGCAAGAAAAGGAGCTGGCCTCTAAATGAGGCTATCATGGCAGTTGGGATGGTGAGCATTTTAGCCAGTTCTCTCTTAAAGAATGACATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCCGCCGATGTCAAATGGGAAGATCAGGCAGAGATATCAGGGAGCAGTCCAATTCTGTCAATAACAATATCAGAAGATGGTAGCATGTCAATAAAGAATGAAGAGGAAGAGCAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCGGTATCAATACCAATCACAGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCTGGAGTGTTGTGGGATGTCCCTTCACCCCCACCCGTGGGAAAGGCTGAACTGGAAGATGGAGCCTACAGAATCAAGCAAAAAGGGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCACACAATGTGGCACGTCACACGTGGCGCTGTCCTAATGCATAAAGGGAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGCTAGAAGGAGAATGGAAAGAAGGAGAAGAAGTCCAGGTCTTGGCATTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACAAAACCTGGCCTTTTCAAAACCAACACCGGAACCATAGGTGCCGTATCTCTGGACTTTTCCCCTGGAACGTCAGGATCTCCAATCGTCGACAAAAAAGGAAAAGTTGTGGGTCTCTATGGCAATGGTGTCGTTACAAGGAGTGGAGCATATGTGAGTGCCATAGCCCAGACTGAAAAAAGCATTGAAGACAATCCAGAGATTGAAGATGACATCTTTCGAAAGAAAAGATTGACCATCATGGACCTCCACCCAGGAGCGGGAAAGACAAAGAGATACCTCCCAGCCATAGTCAGAGAAGCCATAAAAAGAGGCTTGAGAACACTAATCCTGGCCCCCACTAGAGTCGTGGCAGCTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAAACCCCAGCCATCAGGGCTGAGCACACCGGGCGGGAGATTGTGGACCTAATGTGTCATGCCACATTTACCATGAGGCTGCTATCACCAATTAGGGTGCCAAATTACAACCTGATCATCATGGACGAAGCCCATTTCACAGACCCAGCAAGCATAGCAGCTAGAGGATACATCTCAACTCGAGTAGAGATGGGTGAAGCAGCTGGAATTTTTATGACAGCCACTCCTCCGGGTAGCAGAGACCCATTTCCTCAGAGCAATGCACCAATCATGGACGAAGAAAGAGAAATTCCTGAACGTTCGTGGAATTCCGGACATGAGTGGGTCACGGATTTTAAAGGGAAGACTGTTTGGTTTGTTCCAAGCATAAAAGCCGGAAATGACATAGCAGCCTGCCTGAGAAAAAATGGAAAGAGAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAATATGTCAAGACTAGAACCAATGACTGGGACTTCGTGGTCACAACTGACATCTCGGAAATGGGTGCCAACTTCAAAGCTGAGAGGGTTATAGACCCCAGACGCTGCATGAAACCAGTTATACTGACAGATGGTGAAGAGCGGGTGATCCTGGCAGGACCCATGCCAGTGACCCACTCTAGTGCAGCACAAAGAAGAGGGAGAATAGGAAGGAATCCAAAAAATGAAAATGACCAATACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAGGAAGCTAAGATGCTCCTAGATAACATCAACACACCTGAAGGAATCATTCCTAGCATGTTCGAGCCAGAGCGTGAAAAGGTGGATGCCATTGACGGTGAATACCGCTTGAGAGGAGAAGCAAGGAAAACCTTTGTGGACCTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCTTACAAAGTGGCAGCTGAAGGCATCAACTACGCAGACAGAAGGTGGTGTTTTGATGGAATCAGAAACAATCAAATCTTGGAAGAAAATGTGGAAGTGGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTAAAACCCAGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTCAAGGAATTTGCAGCCGGAAGAAAGTCCCTAACCCTGAACCTAATCACAGAGATGGGTAGGCTCCCAACTTTCATGACTCAGAAGGCAAGAGATGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAAGCAGGTGGAAGGGCATACAATCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTGCTGACACTTTTGGCCACAGTCACGGGAGGAATCTTTCTATTCTTGATGAGCGGAAGGGGTATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCCAGCATCCTCCTATGGTACGCACAAATACAGCCACATTGGATAGCAGCTTCAATAATACTGGAGTTCTTTCTCATAGTCTTGCTCATTCCAGAACCAGAAAAGCAGAGAACACCCCAGGATAACCAATTGACCTATGTTGTCATAGCCATCCTCACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTCCTGGAAAAAACAAAGAAAGACCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGCAACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACAACATTTATCACACCAATGTTGAGACATAGCATTGAAAATTCCTCAGTGAATGTGTCCCTAACAGCCATTGCCAACCAAGCCACAGTGCTAATGGGTCTTGGGAAAGGATGGCCATTGTCAAAGATGGACATCGGAGTTCCCCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATAACCCTCACAGCAGCTCTTCTTTTATTGGTAGCACATTATGCCATCATAGGACCAGGACTCCAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGCAGCAGCGGGCATCATGAAAAACCCAACTGTGGATGGAATAACAGTGATTGACCTAGATCCAATACCCTATGATCCAAAGTTTGAAAAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTGCTGATGATGAGGACTACGTGGGCTTTGTGTGAAGCCTTAACCCTAGCAACCGGGCCCATATCCACATTGTGGGAAGGAAATCCAGGGAGATTCTGGAACACAACCATTGCAGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCCATCATGAAGAACACAACCAGCACAAGAAGAGGAACTGGCAACATAGGAGAGACGCTAGGAGAGAAATGGAAAAGCCGACTGAACGCATTGGGGAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGACAGAACCTTAGCAAAAGAAGGCATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTCGAAAGAAATATGGTCACACCAGAAGGGAAAGTAGTGGACCTTGGTTGTGGCAGAGGGGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAACCCATCCCCATGTCAACATATGGGTGGAATCTAGTGCGTCTTCAGAGTGGAGTTGACGTTTTCTTCACTCCACCAGAGAAGTGTGACACATTGTTGTGTGACATAGGGGAGTCGTCACCAAATCCCACGGTAGAAGCAGGACGAACACTCAGAGTCCTTAACCTAGTGGAAAATTGGCTGAACAACAACACCCAATTTTGCATAAAGGTTCTCAACCCATACATGCCCTCAGTCATAGAAAAAATGGAAGCACTACAAAGGAAATATGGAGGAGCCTTGGTGAGAAATCCACTCTCACGGAATTCCACACATGAGATGTACTGGGTGTCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGGATGTTGATTAACAGATTCACAATGAGACACAAGAAAGCCACTTACGAGCCAGATGTTGACCTCGGAAGCGGAACCCGCAACATTGGAATTGAAAGTGAGACACCAAACCTAGACATAATTGGAAAAAGAATAGAAAAAATAAAACAAGAGCATGAAACGTCATGGCACTATGACCAAGACCACCCATACAAAACATGGGCTTACCATGGCAGCTATGAAACAAAACAGACTGGATCAGCATCATCCATGGTGAACGGAGTGGTCAGACTGCTGACAAAACCCTGGGACGTCGTTCCCATGGTGACACAGATGGCAATGACAGACACAACTCCTTTTGGACAACAGCGCGTTTTCAAAGAGAAAGTGGACACGAGAACCCAAGAACCAAAAGAAGGCACAAAAAAACTAATGAAAATCACGGCAGAGTGGCTTTGGAAAGAACTAGGAAAGAAAAAGACACCTAGGATGTGCACCAGAGAAGAATTCACAAAAAAGGTGAGAAGCAATGCAGCCTTGGGGGCCATATTCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATGGTAGGTTTTGGGAGCTGGTTGACAAGGAAAGGAATCTCCATCTTGAAGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAACTAGGAGAGTTTGGCAAAGCAAAAGGCAGCAGAGCCATATGGTACATGTGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTGAATGAAGACCATTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGCACAAGCTAGGTTACATCTTAAGAGACGTGAGCAAGAAAGAAGGAGGAGCAATGTATGCCGATGACACCGCAGGCTGGGACACAAGAATCACACTAGAGGACTTAAAAAATGAAGAAATGATAACAAACCACATGGAAGGAGAACACAAGAAACTTGCCGAGGCCATTTTCAAATTAACGTACCAAAACAAGGTGGTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGATATCATATCGAGAAGAGACCAAAGAGGTAGTGGACAAGTTGGCACCTATGGCCTCAATACTTTCACCAATATGGAAGCACAACTAATCAGGCAGATGGAGGGGGAAGGAATCTTCAAAAGCATCCAGCACTTGACAGCCACAGAAGAAATCGCTGTGCAAGATTGGCTAGCAAGAGTGGGGCGTGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTCTAGATGACAGGTTTGCAAGAGCTTTAACAGCTCTAAATGACATGGGAAAGGTTAGGAAAGACATACAACAATGGGAACCCTCAAGAGGATGGAACGATTGGACACAAGTGCCCTTCTGTTCACACCATTTCCATGAGTTAATCATGAAAGATGGTCGCACACTCGTAGTTCCATGTAGAAACCAAGATGAACTGATTGGTAGAGCCCGAATTTCCCAGGGAGCTGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCTTACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGTGATCTCAGGCTGGCGGCAAATGCCATTTGCTCGGCAGTCCCATCACATTGGGTTCCAACAAGCCGGACAACCTGGTCCATACACGCCAGCCATGAATGGATGACGACGGAAGACATGTTGACAGTCTGGAACAGGGTGTGGATCCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCATACCTGGGAAAAAGAGAAGACCAATGGTGCGGCTCACTGATTGGGCTAACAAGCAGGGCCACCTGGGCAAAGAACATCCAAACAGCAATAAATCAAGTCAGATCCCTCATTGGCAATGAGGAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAGGCAGGAGTCCTGTGGTAGAAGACAGAACTAACATGAAACAAGGCTAGAAGTCAGGTCGGATTAAGCCATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCACAAATGCCATAGCTTGAGCAAACTGTGCAGCCTGTAGCTCCACCTGAGAAGGTGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGTGAGATGAAGCTGTAGTCTCACTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/datasets/denv2/tree.json b/nextclade/datasets/denv2/tree.json index 4840a3af..cfc101f5 100644 --- a/nextclade/datasets/denv2/tree.json +++ b/nextclade/datasets/denv2/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Real-time tracking of dengue virus evolution", "updated": "2024-05-25", "build_url": "https://github.com/nextstrain/dengue", "maintainers": [{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": true, "color_by": "clade_membership"}, "genome_annotations": {"nuc": {"end": 10723, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/config/reference_denv2_genome.gb"}, "2K": {"end": 6825, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 6757, "strand": "+", "type": "CDS"}, "C": {"end": 438, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 97, "strand": "+", "type": "CDS"}, "E": {"end": 2421, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 937, "strand": "+", "type": "CDS"}, "M": {"end": 936, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 439, "strand": "+", "type": "CDS"}, "NS1": {"end": 3477, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 2422, "strand": "+", "type": "CDS"}, "NS2A": {"end": 4131, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 3478, "strand": "+", "type": "CDS"}, "NS2B": {"end": 4521, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 4132, "strand": "+", "type": "CDS"}, "NS3": {"end": 6375, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 4522, "strand": "+", "type": "CDS"}, "NS4A": {"end": 6756, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 6376, "strand": "+", "type": "CDS"}, "NS4B": {"end": 7569, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 6826, "strand": "+", "type": "CDS"}, "NS5": {"end": 10269, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 7570, "strand": "+", "type": "CDS"}, "pr": {"end": 711, "seqid": "../phylogenetic/config/reference_denv2_genome.gb", "start": 439, "strand": "+", "type": "CDS"}}, "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Saudi Arabia", "#5E1D9D"], ["Pakistan", "#4B25B0"], ["India", "#472EB9"], ["Sri Lanka", "#4432BD"], ["Nepal", "#4236C1"], ["Bangladesh", "#403BC5"], ["Myanmar", "#4040C6"], ["Thailand", "#3F45C8"], ["Malaysia", "#3F4BCA"], ["Laos", "#3F50CC"], ["Singapore", "#3F56CE"], ["China", "#3E5BD0"], ["Cambodia", "#3F60D0"], ["Vietnam", "#4065CF"], ["Indonesia", "#416ACF"], ["Brunei", "#426FCE"], ["Taiwan", "#4274CE"], ["Philippines", "#4379CD"], ["South Korea", "#4681C9"], ["French Polynesia", "#4989C4"], ["Palau", "#4B8DC2"], ["Australia", "#4C91BF"], ["Papua New Guinea", "#4E95BD"], ["Fiji", "#56A0AE"], ["Senegal", "#59A3AA"], ["Guinea", "#5BA6A7"], ["Mauritania", "#5DA8A3"], ["C\u00f4te d'Ivoire", "#60AA9F"], ["Burkina Faso", "#65AD96"], ["Ghana", "#68AF92"], ["Benin", "#6EB38A"], ["Niger", "#74B582"], ["Cameroon", "#7EB976"], ["Angola", "#81BA72"], ["Democratic Republic of the Congo", "#85BA6F"], ["Egypt", "#89BB6B"], ["Mozambique", "#90BC65"], ["Tanzania", "#94BD62"], ["Kenya", "#98BD5E"], ["Djibouti", "#9FBE59"], ["Somalia", "#A3BE57"], ["Seychelles", "#A7BE54"], ["France", "#BABC4A"], ["Paraguay", "#CBB742"], ["Brazil", "#D1B440"], ["Peru", "#D3B23F"], ["Ecuador", "#D6B03E"], ["Colombia", "#D9AE3E"], ["Suriname", "#DCAC3D"], ["Guyana", "#DDA83C"], ["Venezuela", "#DFA53B"], ["Panama", "#E39A39"], ["Costa Rica", "#E59738"], ["Nicaragua", "#E68E36"], ["Honduras", "#E67431"], ["Guatemala", "#E4682F"], ["Guadeloupe", "#E3622D"], ["Belize", "#E25B2C"], ["Saint Kitts and Nevis", "#E1552B"], ["Jamaica", "#E04E2A"], 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"AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAACGTAGTTCTAACAGTTTTTTAATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCGAAAAACACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAGCTGACAAAGAGATTCTCACTTGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATATTGAAGAGATGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAGGAAAGAGATTGGAAGGATGCTGAACATCTTGAATAGGAGACGCAGATCTGCAGGCATGATCATTATGCTGATTCCAACAGTGATGGCGTTCCATTTAACCACACGTAACGGAGAACCACACATGATCGTCAGCAGACAAGAGAAAGGGAAAAGTCTTCTGTTTAAAACAGAGGATGGCGTGAACATGTGTACCCTCATGGCCATGGACCTTGGTGAATTGTGTGAAGACACAATCACGTACAAGTGTCCCCTTCTCAGGCAGAATGAGCCAGAAGACATAGACTGTTGGTGCAACTCTACGTCCACGTGGGTAACTTATGGGACGTGTACCACCATGGGAGAACATAGAAGAGAAAAAAGATCAGTGGCACTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGTCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTCACCATGATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATTTTCATCTTACTGACAGCTGTCACTCCTTCAATGACAATGCGTTGCATAGGAATGTCAAATAGAGACTTTGTGGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGAAGCTGTGTGACGACGATGGCAAAAAACAAACCAACATTGGATTTTGAACTGATAAAAACAGAAGCCAAACAGCCTGCCACCCTAAGGAAGTACTGTATAGAGGCAAAGCTAACCAACACAACAACAGAATCTCGCTGCCCAACACAAGGGGAACCCAGCCTAAATGAAGAGCAGGACAAAAGGTTCGTCTGCAAACACTCCATGGTAGACAGAGGATGGGGAAATGGATGTGGACTATTTGGAAAGGGAGGCATTGTGACCTGTGCTATGTTCAGATGCAAAAAGAACATGGAAGGAAAAGTTGTGCAACCAGAAAACTTGGAATACACCATTGTGATAACACCTCACTCAGGGGAAGAGCATGCAGTCGGAAATGACACAGGAAAACATGGCAAGGAAATCAAAATAACACCACAGAGTTCCATCACAGAAGCAGAATTGACAGGTTATGGCACTGTCACAATGGAGTGCTCTCCAAGAACGGGCCTCGACTTCAATGAGATGGTGTTGCTGCAGATGGAAAATAAAGCTTGGCTGGTGCACAGGCAATGGTTCCTAGACCTGCCGTTACCATGGTTGCCCGGAGCGGACACACAAGGGTCAAATTGGATACAGAAAGAGACATTGGTCACTTTCAAAAATCCCCATGCGAAGAAACAGGATGTTGTTGTTTTAGGATCCCAAGAAGGGGCCATGCACACAGCACTTACAGGGGCCACAGAAATCCAAATGTCATCAGGAAACTTACTCTTCACAGGACATCTCAAGTGCAGGCTGAGAATGGACAAGCTACAGCTCAAAGGAATGTCATACTCTATGTGCACAGGAAAGTTTAAAGTTGTGAAGGAAATAGCAGAAACACAACATGGAACAATAGTTATCAGAGTGCAATATGAAGGGGACGGCTCTCCATGCAAGATCCCTTTTGAGATAATGGATTTGGAAAAAAGACATGTCTTAGGTCGCCTGATTACAGTCAACCCAATTGTGACAGAAAAAGATAGCCCAGTCAACATAGAAGCAGAACCTCCATTCGGAGACAGCTACATCATCATAGGAGTAGAGCCGGGACAACTGAAGCTCAACTGGTTTAAGAAAGGAAGTTCTATCGGCCAAATGTTTGAGACAACAATGAGGGGGGCGAAGAGAATGGCCATTTTAGGTGACACAGCCTGGGATTTTGGATCCTTGGGAGGAGTGTTTACATCTATAGGAAAGGCTCTCCACCAAGTCTTTGGAGCAATCTATGGAGCTGCCTTCAGTGGGGTTTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATGAATTCACGCAGCACCTCACTGTCTGTGACACTAGTATTGGTGGGAATTGTGACACTGTATTTGGGAGTCATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAATGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGGACAGAACAATACAAGTTCCAACCAGAATCCCCTTCAAAACTAGCTTCAGCTATCCAGAAAGCCCATGAAGAGGGCATTTGTGGAATCCGCTCAGTAACAAGACTGGAGAATCTGATGTGGAAACAAATAACACCAGAATTGAATCACATTCTATCAGAAAATGAGGTGAAGTTAACTATTATGACAGGAGACATCAAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCTCAGCCCACTGAGCTGAAGTATTCATGGAAAACATGGGGCAAAGCAAAAATGCTCTCTACAGAGTCTCATAACCAGACCTTTCTCATTGATGGCCCCGAAACAGCAGAATGCCCCAACACAAATAGAGCTTGGAATTCGTTGGAAGTTGAAGACTATGGCTTTGGAGTATTCACCACCAATATATGGCTAAAATTGAAAGAAAAACAGGATGTATTCTGCGACTCAAAACTCATGTCAGCGGCCATAAAAGACAACAGAGCCGTCCATGCCGATATGGGTTATTGGATAGAAAGTGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAACTGCCACTGGCCAAAATCACACACCCTCTGGAGCAATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATCTCGCTGGACCAGTGTCTCAACACAACTATAGACCAGGCTACCATACACAAATAACAGGACCATGGCATCTAGGTAAGCTTGAGATGGACTTTGATTTCTGTGATGGAACAACAGTGGTAGTGACTGAGGACTGCGGAAATAGAGGACCCTCTTTGAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGCCGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGGTGCTGGTACGGGATGGAAATCAGACCATTGAAGGAGAAAGAAGAGAATTTGGTCAACTCCTTGGTCACAGCTGGACATGGGCAGGTCGACAACTTTTCACTAGGAGTCTTGGGAATGGCATTGTTCCTGGAGGAAATGCTTAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTTGTGACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTAGGCGCCACTATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCCTACTAGCAGCCTTCAAAGTCAGACCAACTTTTGCAGCTGGACTACTCTTGAGAAAGCTGACCTCCAAGGAATTGATGATGACTACTATAGGAATTGTACTCCTCTCCCAGAGCACCATACCAGAGACCATTCTTGAGTTGACTGATGCGTTAGCCTTAGGCATGATGGTCCTCAAAATGGTGAGAAATATGGAAAAGTATCAATTGGCAGTGACTATCATGGCTATCTTGTGCGTCCCAAACGCAGTGATATTACAAAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCCGTTTCCCCACTGCTCTTAACATCCTCACAGCAAAAAACAGATTGGATACCATTAGCATTGACGATCAAAGGTCTCAATCCAACAGCTATTTTTCTAACAACCCTCTCAAGAACCAGCAAGAAAAGGAGCTGGCCATTAAATGAGGCTATCATGGCAGTCGGGATGGTGAGCATTTTAGCCAGTTCTCTCCTAAAAAATGATATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCAGCCGATGTCAAATGGGAAGACCAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAATGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCCGGAGTATTGTGGGATGTTCCTTCACCCCCACCCATGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATTAAGCAAAAAGGGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCATACAATGTGGCATGTCACACGTGGCGCTGTTCTAATGCATAAAGGAAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGTTAGAAGGAGAATGGAAGGAAGGAGAAGAAGTCCAGGTATTGGCACTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACGAAACCTGGTCTTTTCAAAACCAACGCCGGAACAATAGGTGCTGTATCTCTGGACTTTTCTCCTGGAACGTCAGGATCTCCAATTATCGACAAAAAAGGAAAAGTTGTGGGTCTTTATGGTAATGGTGTTGTTACAAGGAGTGGAGCATATGTGAGTGCTATAGCCCAGACTGAAAAAAGCATTGAAGACAACCCAGAGATCGAAGATGACATTTTCCGAAAGAGAAGACTGACCATCATGGACCTCCACCCAGGAGCGGGAAAGACGAAGAGATACCTTCCGGCCATAGTCAGAGAAGCTATAAAACGGGGTTTGAGAACATTAATCTTGGCCCCCACTAGAGTTGTGGCAGCTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAGACCCCAGCCATCAGAGCTGAGCACACCGGGCGGGAGATTGTGGACCTAATGTGTCATGCCACATTTACCATGAGGCTGCTATCACCAGTTAGAGTGCCAAACTACAACCTGATTATCATGGACGAAGCCCATTTCACAGACCCAGCAAGTATAGCAGCTAGAGGATACATCTCAACTCGAGTGGAGATGGGTGAGGCAGCTGGGATTTTTATGACAGCCACTCCCCCGGGAAGCAGAGACCCATTTCCTCAGAGCAATGCACCAATCATAGATGAAGAAAGAGAAATCCCTGAACGTTCGTGGAATTCCGGACATGAATGGGTCACGGATTTTAAAGGGAAGACTGTTTGGTTCGTTCCAAGTATAAAAGCAGGAAATGATATAGCAGCTTGCCTGAGGAAAAATGGAAAGAAAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAGTATGTCAAGACTAGAACCAATGATTGGGACTTCGTGGTTACAACTGACATTTCAGAAATGGGTGCCAATTTCAAGGCTGAGAGGGTTATAGACCCCAGACGCTGCATGAAACCAGTCATACTAACAGATGGTGAAGAGCGGGTGATTCTGGCAGGACCTATGCCAGTGACCCACTCTAGTGCAGCACAAAGAAGAGGGAGAATAGGAAGAAATCCAAAAAATGAGAATGACCAGTACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAAGAAGCTAAAATGCTCCTAGATAACATCAACACGCCAGAAGGAATCATTCCTAGCATGTTCGAACCAGAGCGTGAAAAGGTGGATGCCATTGATGGCGAATACCGCTTGAGAGGAGAAGCAAGGAAAACCTTTGTAGACTTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCCTACAGAGTGGCAGCTGAAGGCATCAACTACGCAGACAGAAGGTGGTGTTTTGATGGAGTCAAGAACAACCAAATCCTAGAAGAAAACGTGGAAGTTGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTGAAACCCAGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTTAAGGAATTTGCAGCCGGAAGAAAGTCTCTGACCCTGAACCTAATCACAGAAATGGGTAGGCTCCCAACCTTCATGACTCAGAAGGCAAGAGACGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAGGCAGGTGGAAGGGCGTACAACCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTACTGACACTTCTGGCTACAGTCACGGGAGGGATCTTTTTATTCTTGATGAGCGGAAGGGGCATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCTAGCATCCTCCTATGGTACGCACAAATACAGCCACACTGGATAGCAGCTTCAATAATACTGGAGTTTTTTCTCATAGTTTTGCTTATTCCAGAACCTGAAAAACAGAGAACACCCCAAGACAACCAACTGACCTACGTTGTCATAGCCATCCTCACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTCCTAGAAAAAACGAAGAAAGATCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGCAACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACAACATTTGTTACACCAATGTTGAGACATAGCATTGAAAATTCCTCAGTGAATGTGTCCCTAACAGCTATAGCCAACCAAGCCACAGTGTTAATGGGTCTCGGGAAAGGATGGCCATTGTCAAAGATGGACATCGGAGTTCCCCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATAACTCTCACAGCAGCTCTTTTCTTATTGGTAGCACATTATGCCATCATAGGGCCAGGACTCCAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGCAGCGGCGGGCATCATGAAAAACCCAACTGTCGATGGAATAACAGTGATTGACCTAGATCCAATACCTTATGATCCAAAGTTTGAAAAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTATTGATGATGAGGACTACATGGGCTCTGTGTGAGGCTTTAACCTTAGCTACCGGGCCCATCTCCACATTGTGGGAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCGGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCTATTATGAAGAACACAACCAACACAAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAATGGAAAAGCCGATTGAACGCATTGGGAAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGATAGAACCTTAGCAAAAGAAGGCATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCACACCAGAAGGGAAAGTAGTGGACCTCGGTTGTGGCAGAGGAGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAACCCATCCCCATGTCAACATATGGGTGGAATCTAGTGCGTCTTCAAAGTGGAGTTGACGTTTTCTTCATCCCGCCAGAAAAGTGTGACACATTATTGTGTGACATAGGGGAGTCATCACCAAATCCCACAGTGGAAGCAGGACGAACACTCAGAGTCCTTAACTTAGTAGAAAATTGGTTGAACAACAACACTCAATTTTGCATAAAGGTTCTCAACCCATATATGCCCTCAGTCATAGAAAAAATGGAAGCACTACAAAGGAAATATGGAGGAGCCTTAGTGAGGAATCCACTCTCACGAAACTCCACACATGAGATGTACTGGGTATCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGGATGTTGATCAACAGATTTACAATGAGATACAAGAAAGCCACTTACGAGCCGGATGTTGACCTCGGAAGCGGAACCCGTAACATCGGGATTGAAAGTGAGATACCAAACCTAGATATAATTGGGAAAAGAATAGAAAAAATAAAGCAAGAGCATGAAACATCATGGCACTATGACCAAGACCACCCATACAAAACGTGGGCATACCATGGTAGCTATGAAACAAAACAGACTGGATCAGCATCATCCATGGTCAACGGAGTGGTCAGGCTGCTGACAAAACCTTGGGACGTCGTCCCCATGGTGACACAGATGGCAATGACAGACACGACTCCATTTGGACAACAGCGCGTTTTTAAAGAGAAAGTGGACACGAGAACCCAAGAACCGAAAGAAGGCACGAAGAAACTAATGAAAATAACAGCAGAGTGGCTTTGGAAAGAATTAGGGAAGAAAAAGACACCCAGGATGTGCACCAGAGAAGAATTCACAAGAAAGGTGAGAAGCAATGCAGCCTTGGGGGCCATATTCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATAGTAGGTTTTGGGAGCTGGTTGACAAGGAAAGGAATCTCCATCTTGAAGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAGCTAGGGGAATTCGGCAAGGCAAAAGGCAGCAGAGCCATATGGTACATGTGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTAAATGAAGATCACTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGCACAAGCTAGGTTACATTCTAAGAGACGTGAGCAAGAAAGAGGGAGGAGCAATGTATGCCGATGACACCGCAGGATGGGATACAAGAATCACACTAGAAGACCTAAAAAATGAAGAAATGGTAACAAACCACATGGAAGGAGAACACAAGAAACTAGCCGAGGCCATTTTCAAACTAACGTACCAAAACAAGGTGGTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGACATCATATCGAGAAGAGACCAAAGAGGTAGTGGACAAGTTGGCACCTATGGACTCAATACTTTCACCAATATGGAAGCCCAACTAATCAGACAGATGGAGGGAGAAGGAGTCTTTAAAAGCATTCAGCACCTAACAATCACAGAAGAAATCGCTGTGCAAAACTGGTTAGCAAGAGTGGGGCGCGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTTTAGATGACAGGTTCGCAAGCGCTTTAACAGCTCTAAATGACATGGGAAAGATTAGGAAAGACATACAACAATGGGAACCTTCAAGAGGATGGAATGATTGGACACAAGTGCCCTTCTGTTCACACCATTTCCATGAGTTAATCATGAAAGACGGTCGCGTACTCGTTGTTCCATGTAGAAACCAAGATGAACTGATTGGCAGAGCCCGAATCTCCCAAGGAGCAGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCTTACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGCGACCTCAGGCTGGCGGCAAATGCTATTTGCTCGGCAGTACCATCACATTGGGTTCCAACAAGTCGAACAACCTGGTCCATACATGCTAAACATGAATGGATGACAACGGAAGACATGCTGACAGTCTGGAACAGGGTGTGGATTCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCATACTTGGGGAAAAGAGAAGACCAATGGTGCGGCTCATTGATTGGGTTAACAAGCAGGGCCACCTGGGCAAAGAACATCCAAGCAGCAATAAATCAAGTTAGATCCCTTATAGGCAATGAAGAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAAGCAGGAGTTCTGTGGTAGAAAGCAAAACTAACATGAAACAAGGCTAGAAGTCAGGTCGGATTAAGCCATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCATAAATGCCATAGCTTGAGTAAACTATGCAGCCTGTAGCTCCACCTGAGAAGGTGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGCGAGATGAAGCTGTAGTCTCGCTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCGAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT", "2K": "TPQDNQLTYVVIAILTVVAATMA", "C": "MNNQRKKAKNTPFNMLKRERNRVSTVQQLTKRFSLGMLQGRGPLKLFMALVAFLRFLTIPPTAGILKRWGTIKKSKAINVLRGFRKEIGRMLNILNRRRRSAGMIIMLIPTVMA", "E": "MRCIGMSNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVTLVLVGIVTLYLGVMVQA", "M": "FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTITYKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTMGEHRREKRSVALVPHVGMGLETRTETWMSSEGAWKHVQRIETWILRHPGFTMMAAILAYTIGTTHFQRALIFILLTAVTPSMT", "NS1": "DSGCVVSWKNKELKCGSGIFITDNVHTWTEQYKFQPESPSKLASAIQKAHEEGICGIRSVTRLENLMWKQITPELNHILSENEVKLTIMTGDIKGIMQAGKRSLRPQPTELKYSWKTWGKAKMLSTESHNQTFLIDGPETAECPNTNRAWNSLEVEDYGFGVFTTNIWLKLKEKQDVFCDSKLMSAAIKDNRAVHADMGYWIESALNDTWKIEKASFIEVKNCHWPKSHTLWSNGVLESEMIIPKNLAGPVSQHNYRPGYHTQITGPWHLGKLEMDFDFCDGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYRGEDGCWYGMEIRPLKEKEENLVNSLVTA", "NS2A": "GHGQVDNFSLGVLGMALFLEEMLRTRVGTKHAILLVAVSFVTLITGNMSFRDLGRVMVMVGATMTDDIGMGVTYLALLAAFKVRPTFAAGLLLRKLTSKELMMTTIGIVLLSQSTIPETILELTDALALGMMVLKMVRNMEKYQLAVTIMAILCVPNAVILQNAWKVSCTILAVVSVSPLLLTSSQQKTDWIPLALTIKGLNPTAIFLTTLSRTSKKR", "NS2B": "SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIRTGLLVISGLFPVSIPITAAAWYLWEVKKQR", "NS3": "AGVLWDVPSPPPMGKAELEDGAYRIKQKGILGYSQIGAGVYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPIIDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIEDDIFRKRRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPVRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIIDEEREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYVKTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRIGRNPKNENDQYIYMGEPLENDEDCAHWKEAKMLLDNINTPEGIIPSMFEPEREKVDAIDGEYRLRGEARKTFVDLMRRGDLPVWLAYRVAAEGINYADRRWCFDGVKNNQILEENVEVEIWTKEGERKKLKPRWLDARIYSDPLALKEFKEFAAGRK", "NS4A": "SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPETLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQIQPHWIAASIILEFFLIVLLIPEPEKQR", "NS4B": "NEMGFLEKTKKDLGLGSIATQQPESNILDIDLRPASAWTLYAVATTFVTPMLRHSIENSSVNVSLTAIANQATVLMGLGKGWPLSKMDIGVPLLAIGCYSQVNPITLTAALFLLVAHYAIIGPGLQAKATREAQKRAAAGIMKNPTVDGITVIDLDPIPYDPKFEKQLGQVMLLVLCVTQVLMMRTTWALCEALTLATGPISTLWEGNPGRFWNTTIAVSMANIFRGSYLAGAGLLFSIMKNTTNTRR", "NS5": "GTGNIGETLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAKLRWFVERNMVTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFIPPEKCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRYKKATYEPDVDLGSGTRNIGIESEIPNLDIIGKRIEKIKQEHETSWHYDQDHPYKTWAYHGSYETKQTGSASSMVNGVVRLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTQEPKEGTKKLMKITAEWLWKELGKKKTPRMCTREEFTRKVRSNAALGAIFTDENKWKSAREAVEDSRFWELVDKERNLHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWFSRENSLSGVEGEGLHKLGYILRDVSKKEGGAMYADDTAGWDTRITLEDLKNEEMVTNHMEGEHKKLAEAIFKLTYQNKVVRVQRPTPRGTVMDIISRRDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGVFKSIQHLTITEEIAVQNWLARVGRERLSRMAISGDDCVVKPLDDRFASALTALNDMGKIRKDIQQWEPSRGWNDWTQVPFCSHHFHELIMKDGRVLVVPCRNQDELIGRARISQGAGWSLRETACLGKSYAQMWSLMYFHRRDLRLAANAICSAVPSHWVPTSRTTWSIHAKHEWMTTEDMLTVWNRVWIQENPWMEDKTPVESWEEIPYLGKREDQWCGSLIGLTSRATWAKNIQAAINQVRSLIGNEEYTDYMPSMKRFRREEEEAGVLW", "pr": 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"AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAACGTAGTTCTAACAGTTTTTTGATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCGAGAAATACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTACAACAGCTGACAAAGAGATTCTCACTTGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATACTGAAAAGATGGGGAACAATCAAAAAATCAAAGGCTATCAATGTCCTGAGAGGGTTCAGGAAAGAGATTGGAAGGATGCTGAACATCTTGAACAGGAGACGCAGAACTGCAGGCATGATCATCATGCTGATTCCAACAGTGATGGCGTTCCATTTGACCACACGCAACGGAGAACCACACATGATTGTCAGTAGACAAGAGAAAGGGAAAAGCCTTCTGTTTAAAACAGAGGATGGTATGAACATGTGTACCCTCATGGCCATGGACCTTGGTGAGTTGTGTGAAGACACAATCACGTACAAGTGTCCTTTTCTCAGGCAGAACGAACCAGAAGACATAGATTGTTGGTGCAACTCCACGTCCACATGGGTAACTTATGGGACATGTACCACCACAGGAGAGCACAGAAGAGAAAAAAGATCAGTGGCACTTGTTCCACACGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGCCCAGAGAATTGAAACTTGGATTCTGAGACATCCAGGCTTTACCATAATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGTCCTGATTTTCATCTTACTGACAGCCGTCGCTCCTTCAATGACAATGCGCTGCATAGGAATATCAAATAGAGACTTTGTGGAAGGAGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGAAGCTGTGTGACGACGATGGCAAAAAACAAACCAACATTGGACTTTGAACTGATAAAAACAGAAGCCAAACAACCTGCCACTCTAAGGAAGTACTGTATAGAGGCTAAACTGACCAACACAACAACAGAATCTCGCTGCCCAACACAAGGGGAACCCAGCCTAAATGAAGAGCAGGACAAAAGGTTCGTCTGCAAACACTCCATGGTAGACAGAGGATGGGGAAATGGATGTGGATTATTTGGAAAAGGAGGCATTGTGACCTGTGCTATGTTCACATGCAAAAAGAACATGGAAGGAAAAGTTGTGCAGCCAGAAAACTTGGAATACACCATTGTGATAACACCTCACTCAGGGGAAGAACATGCAGTCGGAAATGACACAGGAAAACATGGCAAGGAAGTCAAGATAACACCACAGAGCTCCATCACAGAAGCAGAACTGACAGGCTATGGCACTGTCACGATGGAGTGCTCTCCGAGAACGGGCCTCGACTTCAATGAGATGGTGTTGCTGCAAATGGAAAACAAAGCTTGGCTGGTGCACAGACAATGGTTCCTAGACCTACCGTTACCATGGCTGCCCGGAGCAGACACACAAGGATCAAATTGGATACAGAAAGAGACATTGGTCACTTTCAAAAATCCCCATGCGAAAAAACAGGATGTTGTTGTCTTAGGATCCCAAGAGGGGGCCATGCACACAGCACTCACAGGGGCCACAGAAATCCAGATGTCATCAGGAAACTTACTGTTCACAGGACATCTCAAGTGCAGGCTGAGAATGGACAAACTACAGCTCAAAGGGATGTCATACTCTATGTGCACAGGAAAGTTTAAAGTTGTGAAGGAAATAGCAGAAACACAACATGGAACAATAGTCATCAGAGTACAATATGAAGGAGACGGCTCTCCATGCAAGATCCCTTTTGAGATAATGGATTTGGAAAAAAGACATGTCTTAGGTCGCCTGATCACAGTCAACCCAATTGTAACAGAAAAAGACAGCCCAGTCAACATAGAAGCAGAACCTCCATTCGGAGACAGCTACATCATCATAGGAGTGGAACCAGGACAATTGAAGCTCAACTGGTTTAAGAAAGGAAGTTCTATCGGCCAAATGTTTGAGACAACAATGAGAGGAGCGAAAAGAATGGCCATTTTGGGTGACACAGCCTGGGATTTTGGATCCCTGGGAGGAGTGTTCACATCTATAGGAAAGGCTCTCCACCAAGTTTTTGGAGCAATCTATGGGGCTGCCTTCAGTGGGGTCTCATGGACTATGAAGATCCTCATAGGAGTTATCATCACATGGATAGGAATGAATTCACGCAGCACCTCACTGTCTGTGTCACTAGTATTAGTGGGAATCGTGACACTATACTTGGGAGTTATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAGAACAAAGAACTGAAATGTGGCAGTGGGATTTTCGTCACAGACAACGTGCACACATGGACAGAACAATACAAGTTCCAACCAGAATCCCCTTCAAAACTGGCTTCAGCCATCCAGAAAGCTCATGAAGAGGGCATTTGTGGAATCCGCTCAGTAACAAGACTGGAGAATCTGATGTGGAAACAGATAACACCAGAATTGAATCACATTCTATCAGAAAATGAAGTAAAGCTGACCATCATGACAGGAGACATTAAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCCCAACCCACTGAGCTGAGGTATTCATGGAAAACATGGGGCAAAGCGAAAATGCTCTCCACAGAGCTCCATAATCAGACCTTTCTCATTGATGGTCCCGAAACAGCAGAATGCCCCAACACAAACAGAGCTTGGAATTCACTGGAAGTTGAGGACTATGGCTTTGGAGTATTCACCACCAATATATGGCTAAAATTGAGAGAAAAGCAGGATGTATTTTGTGACTCAAAACTCATGTCAGCGGCCATAAAGGACAACAGAGCCGTCCATGCTGATATGGGTTATTGGATAGAAAGCGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAGCTGCCACTGGCCAAAGTCACACACCCTCTGGAGTAATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATTTCGCTGGACCAGTGTCACAACACAACTACAGACCAGGCTATTACACACAAACAGCAGGACCTTGGCATCTAGGCAAGCTTGAGATGGACTTTGATTTCTGCGAAGGAACTACAGTGGTGGTGACCGAGGACTGTGGAAACAGAGGACCCTCTTTAAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGCCGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGATGCTGGTACGGGATGGAAATCAGACCATTGAAAGAGAAAGAAGAGAATCTGGTCAACTCTTTGGTCACAGCCGGACATGGGCAGATTGACAACTTTTCACTAGGAATCTTGGGAATGGCATTGTTCCTGGAAGAAATGCTCAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTCGTGACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTGGGCGCTACCATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCCTACTAGCAGCTTTCAAAGTCAGACCAACCTTTGCAGCTGGACTGCTCTTGAGAAAACTGACCTCCAAGGAATTGATGATGACCACCATAGGAATCGTTCTCCTCTCCCAGAGTAGCATACCAGAGACCATTCTTGAACTGACTGATGCGTTAGCCTTGGGCATGATGGTCCTCAAAATAGTGAGAAACATGGAAAAATATCAGCTGGCAGTGACCATCATGGCTATCTTATGCGTCCCAAATGCTGTGATATTACAGAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCTGTTTCCCCACTGCTCTTAACATCCTCACAACAGAAAGCGGATTGGATACCATTAGCATTGACGATCAAAGGTCTCAATCCAACAGCCATTTTTCTAACAACCCTTTCAAGAACCAGCAAGAAAAGGAGCTGGCCTCTAAATGAGGCTATCATGGCAGTTGGGATGGTGAGCATTTTAGCCAGTTCTCTCTTAAAGAATGACATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCCGCCGATGTCAAATGGGAAGATCAGGCAGAGATATCAGGGAGCAGTCCAATTCTGTCAATAACAATATCAGAAGATGGTAGCATGTCAATAAAGAATGAAGAGGAAGAGCAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCGGTATCAATACCAATCACAGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCTGGAGTGTTGTGGGATGTCCCTTCACCCCCACCCGTGGGAAAGGCTGAACTGGAAGATGGAGCCTACAGAATCAAGCAAAAAGGGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCACACAATGTGGCACGTCACACGTGGCGCTGTCCTAATGCATAAAGGGAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGCTAGAAGGAGAATGGAAAGAAGGAGAAGAAGTCCAGGTCTTGGCATTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACAAAACCTGGCCTTTTCAAAACCAACACCGGAACCATAGGTGCCGTATCTCTGGACTTTTCCCCTGGAACGTCAGGATCTCCAATCGTCGACAAAAAAGGAAAAGTTGTGGGTCTCTATGGCAATGGTGTCGTTACAAGGAGTGGAGCATATGTGAGTGCCATAGCCCAGACTGAAAAAAGCATTGAAGACAATCCAGAGATTGAAGATGACATCTTTCGAAAGAAAAGATTGACCATCATGGACCTCCACCCAGGAGCGGGAAAGACAAAGAGATACCTCCCAGCCATAGTCAGAGAAGCCATAAAAAGAGGCTTGAGAACACTAATCCTGGCCCCCACTAGAGTCGTGGCAGCTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAAACCCCAGCCATCAGGGCTGAGCACACCGGGCGGGAGATTGTGGACCTAATGTGTCATGCCACATTTACCATGAGGCTGCTATCACCAATTAGGGTGCCAAATTACAACCTGATCATCATGGACGAAGCCCATTTCACAGACCCAGCAAGCATAGCAGCTAGAGGATACATCTCAACTCGAGTAGAGATGGGTGAAGCAGCTGGAATTTTTATGACAGCCACTCCTCCGGGTAGCAGAGACCCATTTCCTCAGAGCAATGCACCAATCATGGACGAAGAAAGAGAAATTCCTGAACGTTCGTGGAATTCCGGACATGAGTGGGTCACGGATTTTAAAGGGAAGACTGTTTGGTTTGTTCCAAGCATAAAAGCCGGAAATGACATAGCAGCCTGCCTGAGAAAAAATGGAAAGAGAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAATATGTCAAGACTAGAACCAATGACTGGGACTTCGTGGTCACAACTGACATCTCGGAAATGGGTGCCAACTTCAAAGCTGAGAGGGTTATAGACCCCAGACGCTGCATGAAACCAGTTATACTGACAGATGGTGAAGAGCGGGTGATCCTGGCAGGACCCATGCCAGTGACCCACTCTAGTGCAGCACAAAGAAGAGGGAGAATAGGAAGGAATCCAAAAAATGAAAATGACCAATACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAGGAAGCTAAGATGCTCCTAGATAACATCAACACACCTGAAGGAATCATTCCTAGCATGTTCGAGCCAGAGCGTGAAAAGGTGGATGCCATTGACGGTGAATACCGCTTGAGAGGAGAAGCAAGGAAAACCTTTGTGGACCTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCTTACAAAGTGGCAGCTGAAGGCATCAACTACGCAGACAGAAGGTGGTGTTTTGATGGAATCAGAAACAATCAAATCTTGGAAGAAAATGTGGAAGTGGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTAAAACCCAGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTCAAGGAATTTGCAGCCGGAAGAAAGTCCCTAACCCTGAACCTAATCACAGAGATGGGTAGGCTCCCAACTTTCATGACTCAGAAGGCAAGAGATGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAAGCAGGTGGAAGGGCATACAATCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTGCTGACACTTTTGGCCACAGTCACGGGAGGAATCTTTCTATTCTTGATGAGCGGAAGGGGTATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCCAGCATCCTCCTATGGTACGCACAAATACAGCCACATTGGATAGCAGCTTCAATAATACTGGAGTTCTTTCTCATAGTCTTGCTCATTCCAGAACCAGAAAAGCAGAGAACACCCCAGGATAACCAATTGACCTATGTTGTCATAGCCATCCTCACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTCCTGGAAAAAACAAAGAAAGACCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGCAACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACAACATTTATCACACCAATGTTGAGACATAGCATTGAAAATTCCTCAGTGAATGTGTCCCTAACAGCCATTGCCAACCAAGCCACAGTGCTAATGGGTCTTGGGAAAGGATGGCCATTGTCAAAGATGGACATCGGAGTTCCCCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATAACCCTCACAGCAGCTCTTCTTTTATTGGTAGCACATTATGCCATCATAGGACCAGGACTCCAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGCAGCAGCGGGCATCATGAAAAACCCAACTGTGGATGGAATAACAGTGATTGACCTAGATCCAATACCCTATGATCCAAAGTTTGAAAAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTGCTGATGATGAGGACTACGTGGGCTTTGTGTGAAGCCTTAACCCTAGCAACCGGGCCCATATCCACATTGTGGGAAGGAAATCCAGGGAGATTCTGGAACACAACCATTGCAGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCCATCATGAAGAACACAACCAGCACAAGAAGAGGAACTGGCAACATAGGAGAGACGCTAGGAGAGAAATGGAAAAGCCGACTGAACGCATTGGGGAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGACAGAACCTTAGCAAAAGAAGGCATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTCGAAAGAAATATGGTCACACCAGAAGGGAAAGTAGTGGACCTTGGTTGTGGCAGAGGGGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAACCCATCCCCATGTCAACATATGGGTGGAATCTAGTGCGTCTTCAGAGTGGAGTTGACGTTTTCTTCACTCCACCAGAGAAGTGTGACACATTGTTGTGTGACATAGGGGAGTCGTCACCAAATCCCACGGTAGAAGCAGGACGAACACTCAGAGTCCTTAACCTAGTGGAAAATTGGCTGAACAACAACACCCAATTTTGCATAAAGGTTCTCAACCCATACATGCCCTCAGTCATAGAAAAAATGGAAGCACTACAAAGGAAATATGGAGGAGCCTTGGTGAGAAATCCACTCTCACGGAATTCCACACATGAGATGTACTGGGTGTCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGGATGTTGATTAACAGATTCACAATGAGACACAAGAAAGCCACTTACGAGCCAGATGTTGACCTCGGAAGCGGAACCCGCAACATTGGAATTGAAAGTGAGACACCAAACCTAGACATAATTGGAAAAAGAATAGAAAAAATAAAACAAGAGCATGAAACGTCATGGCACTATGACCAAGACCACCCATACAAAACATGGGCTTACCATGGCAGCTATGAAACAAAACAGACTGGATCAGCATCATCCATGGTGAACGGAGTGGTCAGACTGCTGACAAAACCCTGGGACGTCGTTCCCATGGTGACACAGATGGCAATGACAGACACAACTCCTTTTGGACAACAGCGCGTTTTCAAAGAGAAAGTGGACACGAGAACCCAAGAACCAAAAGAAGGCACAAAAAAACTAATGAAAATCACGGCAGAGTGGCTTTGGAAAGAACTAGGAAAGAAAAAGACACCTAGGATGTGCACCAGAGAAGAATTCACAAAAAAGGTGAGAAGCAATGCAGCCTTGGGGGCCATATTCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATGGTAGGTTTTGGGAGCTGGTTGACAAGGAAAGGAATCTCCATCTTGAAGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAACTAGGAGAGTTTGGCAAAGCAAAAGGCAGCAGAGCCATATGGTACATGTGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTGAATGAAGACCATTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGCACAAGCTAGGTTACATCTTAAGAGACGTGAGCAAGAAAGAAGGAGGAGCAATGTATGCCGATGACACCGCAGGCTGGGACACAAGAATCACACTAGAGGACTTAAAAAATGAAGAAATGATAACAAACCACATGGAAGGAGAACACAAGAAACTTGCCGAGGCCATTTTCAAATTAACGTACCAAAACAAGGTGGTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGATATCATATCGAGAAGAGACCAAAGAGGTAGTGGACAAGTTGGCACCTATGGCCTCAATACTTTCACCAATATGGAAGCACAACTAATCAGGCAGATGGAGGGGGAAGGAATCTTCAAAAGCATCCAGCACTTGACAGCCACAGAAGAAATCGCTGTGCAAGATTGGCTAGCAAGAGTGGGGCGTGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTCTAGATGACAGGTTTGCAAGAGCTTTAACAGCTCTAAATGACATGGGAAAGGTTAGGAAAGACATACAACAATGGGAACCCTCAAGAGGATGGAACGATTGGACACAAGTGCCCTTCTGTTCACACCATTTCCATGAGTTAATCATGAAAGATGGTCGCACACTCGTAGTTCCATGTAGAAACCAAGATGAACTGATTGGTAGAGCCCGAATTTCCCAGGGAGCTGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCTTACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGTGATCTCAGGCTGGCGGCAAATGCCATTTGCTCGGCAGTCCCATCACATTGGGTTCCAACAAGCCGGACAACCTGGTCCATACACGCCAGCCATGAATGGATGACGACGGAAGACATGTTGACAGTCTGGAACAGGGTGTGGATCCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCATACCTGGGAAAAAGAGAAGACCAATGGTGCGGCTCACTGATTGGGCTAACAAGCAGGGCCACCTGGGCAAAGAACATCCAAACAGCAATAAATCAAGTCAGATCCCTCATTGGCAATGAGGAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAGGCAGGAGTCCTGTGGTAGAAGACAGAACTAACATGAAACAAGGCTAGAAGTCAGGTCGGATTAAGCCATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCACAAATGCCATAGCTTGAGCAAACTGTGCAGCCTGTAGCTCCACCTGAGAAGGTGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGTGAGATGAAGCTGTAGTCTCACTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT", "2K": "TPQDNQLTYVVIAILTVVAATMA", "C": "MNNQRKKARNTPFNMLKRERNRVSTVQQLTKRFSLGMLQGRGPLKLFMALVAFLRFLTIPPTAGILKRWGTIKKSKAINVLRGFRKEIGRMLNILNRRRRTAGMIIMLIPTVMA", "E": "MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEVKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVSLVLVGIVTLYLGVMVQA", "M": "FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGMNMCTLMAMDLGELCEDTITYKCPFLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVGMGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQRVLIFILLTAVAPSMT", "NS1": "DSGCVVSWKNKELKCGSGIFVTDNVHTWTEQYKFQPESPSKLASAIQKAHEEGICGIRSVTRLENLMWKQITPELNHILSENEVKLTIMTGDIKGIMQAGKRSLRPQPTELRYSWKTWGKAKMLSTELHNQTFLIDGPETAECPNTNRAWNSLEVEDYGFGVFTTNIWLKLREKQDVFCDSKLMSAAIKDNRAVHADMGYWIESALNDTWKIEKASFIEVKSCHWPKSHTLWSNGVLESEMIIPKNFAGPVSQHNYRPGYYTQTAGPWHLGKLEMDFDFCEGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYRGEDGCWYGMEIRPLKEKEENLVNSLVTA", "NS2A": "GHGQIDNFSLGILGMALFLEEMLRTRVGTKHAILLVAVSFVTLITGNMSFRDLGRVMVMVGATMTDDIGMGVTYLALLAAFKVRPTFAAGLLLRKLTSKELMMTTIGIVLLSQSSIPETILELTDALALGMMVLKIVRNMEKYQLAVTIMAILCVPNAVILQNAWKVSCTILAVVSVSPLLLTSSQQKADWIPLALTIKGLNPTAIFLTTLSRTSKKR", "NS2B": "SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIRTGLLVISGLFPVSIPITAAAWYLWEVKKQR", "NS3": "AGVLWDVPSPPPVGKAELEDGAYRIKQKGILGYSQIGAGVYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNTGTIGAVSLDFSPGTSGSPIVDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIEDDIFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKRVIQLSRKTFDSEYVKTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRIGRNPKNENDQYIYMGEPLENDEDCAHWKEAKMLLDNINTPEGIIPSMFEPEREKVDAIDGEYRLRGEARKTFVDLMRRGDLPVWLAYKVAAEGINYADRRWCFDGIRNNQILEENVEVEIWTKEGERKKLKPRWLDARIYSDPLALKEFKEFAAGRK", "NS4A": "SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPETLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQIQPHWIAASIILEFFLIVLLIPEPEKQR", "NS4B": "NEMGFLEKTKKDLGLGSIATQQPESNILDIDLRPASAWTLYAVATTFITPMLRHSIENSSVNVSLTAIANQATVLMGLGKGWPLSKMDIGVPLLAIGCYSQVNPITLTAALLLLVAHYAIIGPGLQAKATREAQKRAAAGIMKNPTVDGITVIDLDPIPYDPKFEKQLGQVMLLVLCVTQVLMMRTTWALCEALTLATGPISTLWEGNPGRFWNTTIAVSMANIFRGSYLAGAGLLFSIMKNTTSTRR", "NS5": "GTGNIGETLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAKLRWFVERNMVTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFTPPEKCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRHKKATYEPDVDLGSGTRNIGIESETPNLDIIGKRIEKIKQEHETSWHYDQDHPYKTWAYHGSYETKQTGSASSMVNGVVRLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTQEPKEGTKKLMKITAEWLWKELGKKKTPRMCTREEFTKKVRSNAALGAIFTDENKWKSAREAVEDGRFWELVDKERNLHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWFSRENSLSGVEGEGLHKLGYILRDVSKKEGGAMYADDTAGWDTRITLEDLKNEEMITNHMEGEHKKLAEAIFKLTYQNKVVRVQRPTPRGTVMDIISRRDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGIFKSIQHLTATEEIAVQDWLARVGRERLSRMAISGDDCVVKPLDDRFARALTALNDMGKVRKDIQQWEPSRGWNDWTQVPFCSHHFHELIMKDGRTLVVPCRNQDELIGRARISQGAGWSLRETACLGKSYAQMWSLMYFHRRDLRLAANAICSAVPSHWVPTSRTTWSIHASHEWMTTEDMLTVWNRVWIQENPWMEDKTPVESWEEIPYLGKREDQWCGSLIGLTSRATWAKNIQTAINQVRSLIGNEEYTDYMPSMKRFRREEEEAGVLW", "pr": "FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGMNMCTLMAMDLGELCEDTITYKCPFLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKR"}} \ No newline at end of file diff --git a/nextclade/datasets/denv3/genome_annotation.gff3 b/nextclade/datasets/denv3/genome_annotation.gff3 index 709bb930..f0192507 100644 --- a/nextclade/datasets/denv3/genome_annotation.gff3 +++ b/nextclade/datasets/denv3/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_001475.2 1 10707 -NC_001475.2 feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; -NC_001475.2 feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; -NC_001475.2 feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; -NC_001475.2 feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; -NC_001475.2 feature gene 2414 3469 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_001475.2 feature gene 3470 4123 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_001475.2 feature gene 4124 4513 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_001475.2 feature gene 4514 6370 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_001475.2 feature gene 6371 6751 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_001475.2 feature gene 6752 6820 . + . codon_start=1;gene=2K;gene_name=2K; -NC_001475.2 feature gene 6821 7564 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_001475.2 feature gene 7565 10264 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome 1 10707 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 2414 3469 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 3470 4123 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 4124 4513 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 4514 6370 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 6371 6751 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 6752 6820 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 6821 7564 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 7565 10264 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/datasets/denv3/pathogen.json b/nextclade/datasets/denv3/pathogen.json index aad0069c..1db88244 100644 --- a/nextclade/datasets/denv3/pathogen.json +++ b/nextclade/datasets/denv3/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/datasets/denv3/reference.fasta b/nextclade/datasets/denv3/reference.fasta index 8bf6921f..abe0db37 100644 --- a/nextclade/datasets/denv3/reference.fasta +++ b/nextclade/datasets/denv3/reference.fasta @@ -1,180 +1,2 @@ ->NC_001475.2 Dengue virus 3, complete genome -AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGACTCGGAAGCTTGCTTAACGTAG -TGCTGACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAGAAGACGGG -AAAACCGTCTATCAATATGCTGAAACGCGTGAGAAACCGTGTGTCAACTGGATCACAGTT -GGCGAAGAGATTCTCAAAAGGACTGCTGAACGGCCAGGGACCAATGAAATTGGTTATGGC -GTTCATAGCTTTCCTCAGATTTCTAGCCATTCCACCAACAGCAGGAGTCTTGGCTAGATG -GGGAACCTTCAAGAAGTCGGGGGCCATTAAGGTCCTGAAAGGCTTCAAGAAGGAGATCTC -AAACATGCTGAGCATAATCAACCAACGGAAAAAGACATCGCTCTGTCTCATGATGATATT -GCCAGCAGCACTTGCTTTCCACTTGACTTCACGAGATGGAGAGCCGCGCATGATTGTGGG -GAAGAATGAAAGAGGTAAATCCCTACTTTTTAAGACAGCCTCTGGAATCAACATGTGCAC -ACTCATAGCCATGGATTTGGGAGAGATGTGTGATGACACGGTCACTTACAAATGCCCCCA -CATTACCGAAGTGGAACCTGAAGACATTGACTGCTGGTGCAACCTTACATCAACATGGGT -GACTTATGGAACGTGCAATCAAGCTGGAGAGCATAGACGCGACAAGAGATCAGTGGCGTT -AGCTCCCCATGTCGGCATGGGACTGGACACACGCACCCAAACCTGGATGTCGGCTGAAGG -AGCTTGGAGACAAGTCGAGAAGGTAGAGACATGGGCCCTTAGGCACCCAGGGTTCACCAT -ACTAGCCCTATTTCTCGCCCATTACATAGGCACTTCCCTGACCCAGAAGGTGGTTATTTT -CATATTATTAATGCTGGTCACCCCATCCATGACAATGAGATGTGTGGGAGTAGGAAACAG -AGATTTTGTGGAAGGGCTATCAGGAGCTACGTGGGTTGACGTGGTGCTCGAGCACGGGGG -GTGTGTGACTACCATGGCTAAGAACAAGCCCACGCTGGATATAGAGCTTCAGAAGACCGA -GGCCACCCAACTGGCGACCCTAAGGAAGCTATGCATTGAGGGGAAAATTACCAACATAAC -AACTGACTCAAGATGTCCTACCCAAGGGGAAGCGGTTTTGCCTGAGGAGCAGGACCAGAA -CTACGTGTGTAAGCATACATACGTAGACAGAGGTTGGGGGAACGGTTGTGGTTTGTTTGG -CAAAGGAAGCTTGGTAACATGTGCGAAATTTCAATGCCTGGAACCAATAGAGGGAAAAGT -GGTGCAATATGAGAACCTCAAATACACCGTCATCATTACAGTGCACACAGGAGACCAACA -CCAGGTGGGAAATGAAACGCAAGGAGTCACGGCTGAGATAACACCTCAGGCATCAACCAC -TGAAGCCATCTTGCCTGAATATGGAACCCTTGGGCTAGAATGCTCACCACGGACAGGTTT -GGATTTCAATGAAATGATCTTACTAACAATGAAGAACAAAGCATGGATGGTACATAGACA -ATGGTTCTTTGACCTACCTCTACCATGGGCATCAGGAGCTACAACAGAAACACCAACCTG -GAACAGGAAGGAGCTTCTTGTGACATTCAAAAACGCACATGCGAAAAAACAAGAAGTAGT -TGTCCTTGGATCGCAAGAGGGAGCAATGCATACCGCACTGACAGGAGCTACAGAAATCCA -AAACTCAGGAGGCACAAGCATTTTCGCGGGGCACTTAAAATGTAGACTTAAGATGGACAA -ATTGGAACTCAAGGGGATGAGCTATGCAATGTGCACGAATACCTTTGTGTTGAAGAAAGA -AGTCTCAGAAACGCAGCACGGGACAATACTCATTAAGGTTGAGTACAAAGGGGAAGATGC -ACCTTGCAAGATTCCCTTTTCCACAGAGGATGGACAAGGGAAAGCTCATAATGGCAGACT -GATCACAGCCAACCCTGTGGTGACTAAGAAGGAGGAGCCTGTCAATATTGAGGCTGAACC -TCCTTTTGGGGAAAGCAATATAGTAATTGGAATTGGAGACAACGCCTTGAAAATCAACTG -GTACAAGAAGGGGAGCTCGATTGGGAAGATGTTCGAGGCCACTGAAAGGGGTGCAAGGCG -CATGGCCATCTTGGGAGACACAGCTTGGGACTTTGGATCAGTGGGTGGTGTTCTGAACTC -ATTAGGCAAAATGGTGCACCAAATATTTGGAAGTGCTTATACAGCCCTGTTCAGTGGAGT -CTCTTGGGTGATGAAAATTGGAATAGGTGTCCTCTTGACTTGGATAGGGTTGAATTCAAA -AAACACATCCATGTCATTTTCATGCATTGCGATAGGAATCATTACACTCTATCTGGGAGC -TGTGGTACAAGCTGACATGGGGTGTGTCATAAACTGGAAGGGCAAAGAACTCAAATGTGG -AAGCGGAATTTTCGTCACCAATGAGGTCCATACCTGGACAGAGCAATACAAATTCCAAGC -AGACTCCCCAAAAAGATTGGCAACAGCCATTGCAGGCGCCTGGGAGAATGGAGTGTGTGG -AATTAGGTCAACAACCAGAATGGAGAATCTCTTGTGGAAGCAAATAGCCAATGAACTGAA -CTACATATTATGGGAAAACAATATCAAATTAACGGTAGTTGTGGGCGATACACTTGGGGT -CTTAGAGCAAGGGAAAAGAACACTAACACCACAACCCATGGAGCTAAAATACTCATGGAA -AACGTGGGGAAAGGCAAAAATAGTGACAGCTGAAACACAAAATTCCTCTTTCATAATAGA -CGGGCCAAACACACCGGAGTGTCCAAGTGCCTCAAGAGCATGGAATGTGTGGGAGGTGGA -AGATTACGGGTTCGGAGTCTTCACAACCAACATATGGCTGAAACTCCGAGAGGTCTACAC -CCAACTATGTGACCATAGGCTAATGTCGGCAGCTGTCAAGGATGAGAGGGCCGTGCATGC -CGACATGGGCTACTGGATAGAAAGCCAAAAGAATGGAAGTTGGAAGCTAGAAAAAGCATC -CCTCATAGAGGTAAAAACCTGCACATGGCCAAAATCACACACTCTCTGGACTAATGGTGT -GCTAGAGAGTGACATGATCATCCCAAAGAGTCTAGCTGGTCCTATCTCACAACACAACTA -CAGGCCCGGGTACCACACCCAAACGGCAGGACCCTGGCACTTAGGAAAATTGGAGCTGGA -CTTCAACTACTGTGAAGGAACAACAGTTGTCATCACAGAAAGCTGTGGGACAAGAGGCCC -ATCATTGAGAACAACAACAGTGTCAGGGAAGTTGATACACGAATGGTGTTGCCGCTCGTG -CACACTTCCCCCCCTGCGATACATGGGAGAAGACGGCTGCTGGTATGGCATGGAAATCAG -ACCCATCAGTGAGAAAGAAGAGAACATGGTAAAGTCTTTAGTCTCAGCGGGAAGTGGAAA -GGTGGACAACTTCACAATGGGTGTCTTGTGTTTGGCAATCCTCTTTGAAGAGGTGTTGAG -AGGAAAATTTGGGAAGAAACACATGATTGCAGGGGTTTTCTTTACGTTTGTGCTCCTTCT -CTCAGGGCAAATAACATGGAGAGACATGGCGCACACACTAATAATGATCGGGTCCAACGC -CTCTGACAGGATGGGAATGGGCGTCACCTACCTAGCTCTAATTGCAACATTTAAAATCCA -GCCATTCTTGGCTTTGGGATTTTTCCTAAGAAAGCTGACATCTAGAGAAAATTTATTGTT -AGGAGTTGGGTTGGCCATGGCAACAACGTTACAACTGCCAGAGGACATTGAACAAATGGC -AAATGGAGTCGCTCTGGGGCTCATGGCTCTTAAACTGATAACACAATTTGAAACATACCA -ATTGTGGACGGCATTAGTCTCCTTAACGTGTTCAAACACAATTTTTACGTTGACTGTTGC -CTGGAGAACAGCCACTCTGATTTTGGCCGGAGTTTCGCTTTTACCAGTGTGCCAGTCTTC -AAGCATGAGGAAAACAGATTGGCTCCCAATGACAGTGGCAGCTATGGGAGTTCCACCCCT -TCCACTTTTTATTTTTAGCTTGAAAGACACACTCAAAAGGAGAAGCTGGCCACTGAATGA -AGGGGTGATGGCTGTTGGGCTTGTGAGCATTCTGGCCAGTTCTCTCCTTAGAAATGATGT -GCCCATGGCTGGACCATTAGTGGCCGGGGGCTTGCTGATAGCGTGCTACGTCATAACTGG -CACGTCAGCGGACCTCACTGTAGAAAAAGCCCCAGATGTAACATGGGAGGAAGAGGCTGA -GCAGACAGGAGTGTCCCACAACTTAATGATCACAGTTGATGATGATGGAACAATGAGAAT -AAAAGATGATGAGACTGAGAACATCCTAACAGTGCTTTTAAAAACAGCATTACTAATAGT -ATCAGGCATTTTTCCATACTCCATACCCGCAACATTGTTGGTCTGGCACACTTGGCAAAA -ACAAACCCAAAGATCCGGCGTTTTATGGGACGTACCCAGCCCCCCAGAGACACAGAAAGC -AGAACTGGAAGAAGGGGTTTATAGGATCAAACAGCAAGGAATTTTTGGGAAAACCCAAGT -AGGGGTTGGAGTACAGAAAGAAGGAGTCTTCCACACCATGTGGCACGTCACAAGAGGGGC -AGTGTTGACACATAATGGGAAAAGACTGGAACCAAACTGGGCTAGTGTGAAAAAAGATCT -GATTTCATATGGAGGAGGATGGAGACTGAGCGCACAATGGCAAAAGGGGGAGGAGGTGCA -GGTTATTGCCGTAGAGCCAGGGAAGAACCCAAAGAACTTTCAAACCACGCCAGGCACTTT -CCAGACTACTACAGGGGAAATAGGAGCAATTGCACTGGATTTCAAGCCTGGAACTTCAGG -ATCTCCTATCATAAATAGAGAGGGAAAGGTAGTGGGACTGTATGGCAATGGAGTGGTTAC -AAAGAATGGTGGCTATGTCAGCGGAATAGCGCAAACAAATGCAGAACCAGATGGACCGAC -ACCAGAGTTGGAAGAAGAGATGTTCAAAAAGCGAAACCTGACCATAATGGATCTTCATCC -TGGGTCAGGAAAGACACGGAAATACCTTCCAGCTATTGTCAGAGAGGCAATCAAGAGACG -TTTAAGAACCTTAATTTTGGCACCGACAAGGGTGGTTGCAGCTGAGATGGAAGAAGCATT -GAAAGGGCTCCCAATAAGGTACCAAACAACAGCAACAAAATCTGAACACACAGGAAGAGA -GATTGTTGATCTAATGTGCCACGCAACGTTCACAATGCGTTTGCTGTCACCAGTTAGGGT -TCCAAATTACAACTTGATAATAATGGATGAGGCCCATTTCACAGACCCAGCCAGTATAGC -GGCTAGAGGGTACATATCAACTCGTGTTGGAATGGGAGAGGCAGCCGCAATCTTCATGAC -AGCAACACCCCCTGGAACAGCTGATGCCTTTCCTCAGAGCAACGCTCCAATTCAAGATGA -AGAAAGGGACATACCAGAACGCTCATGGAATTCAGGCAATGAATGGATTACCGACTTCGC -TGGGAAAACGGTGTGGTTTGTCCCTAGCATTAAAGCCGGAAATGACATAGCAAACTGCTT -GCGAAAAAACGGGAAAAAAGTCATTCAACTTAGTAGGAAGACTTTTGACACAGAATATCA -GAAGACTAAACTGAATGATTGGGACTTTGTGGTGACAACTGACATTTCAGAAATGGGGGC -CAATTTCAAAGCAGATAGAGTGATCGACCCAAGAAGATGTCTCAAACCAGTGATCTTGAC -AGATGGACCAGAGCGGGTGATCCTGGCCGGACCAATGCCAGTCACCGCGGCGAGTGCTGC -GCAAAGGAGAGGGAGAGTTGGCAGGAACCCACAAAAAGAGAATGACCAGTACATATTCAC -GGGCCAGCCTCTCAACAATGATGAAGACCATGCTCACTGGACAGAAGCAAAAATGCTGCT -GGACAACATCAACACACCAGAAGGGATTATACCAGCTCTCTTTGAACCAGAAAGGGAGAA -GTCAGCCGCCATAGACGGTGAGTATCGCCTGAAGGGTGAGTCCAGGAAGACTTTCGTGGA -ACTCATGAGGAGGGGTGACCTTCCAGTTTGGTTAGCCCATAAAGTAGCATCAGAAGGAAT -CAAATACACAGATAGAAAATGGTGCTTTGATGGGCAACGCAATAATCAAATTTTAGAGGA -GAACATGGATGTGGAAATTTGGACAAAGGAAGGAGAAAAGAAAAAATTGAGACCTAGGTG -GCTTGATGCCCGCACTTATTCAGATCCATTGGCACTCAAGGAATTCAAGGACTTTGCGGC -TGGCAGAAAGTCAATCGCCCTTGATCTTGTGACAGAAATAGGAAGAGTGCCTTCACATCT -AGCCCACAGAACAAGAAACGCTCTGGACAATCTGGTGATGCTGCATACGTCAGAAGATGG -CGGTAGGGCTTACAGGCATGCGGTGGAGGAACTACCAGAAACAATGGAAACACTCCTACT -CTTGGGACTAATGATCTTGTTGACAGGTGGAGCAATGCTTTTCTTGATATCAGGTAAAGG -GATTGGAAAGACTTCAATAGGACTCATTTGTGTAATCGCTTCCAGCGGCATGTTGTGGAT -GGCCGAAGTTCCACTCCAATGGATCGCGTCGGCTATAGTCCTGGAGTTTTTTATGATGGT -GTTGCTCATACCAGAACCAGAAAAGCAGAGAACCCCCCAAGACAACCAACTCGCATATGT -CGTGATAGGCATACTTACATTGGCTGCAACAATAGCAGCCAATGAAATGGGACTGCTGGA -AACCACAAAGAGAGACTTAGGAATGTCTAAGGAGCCAGGTGTTGTTTCTCCAACCAGCTA -TTTGGATGTGGACTTGCACCCAGCATCAGCCTGGACATTGTACGCCGTGGCCACTACAGT -AATAACACCAATGTTAAGACATACCATAGAGAATTCTACAGCAAATGTGTCCCTGGCAGC -TATAGCCAACCAGGCAGTGGTCCTGATGGGTTTGGACAAAGGATGGCCAATATCAAAAAT -GGACTTAGGCGTGCCACTACTGGCACTGGGTTGCTATTCACAAGTGAACCCACTGACTCT -AACTGCGGCAGTACTTTTGCTAATCACACATTATGCTATCATAGGTCCAGGATTGCAAGC -AAAAGCCACCCGTGAAGCTCAGAAAAGGACAGCTGCTGGAATAATGAAGAATCCAACAGT -GGATGGGATAATGACAATAGACCTAGATTCTGTAATATTTGATTCAAAATTTGAAAAACA -ACTGGGACAGGTTATGCTCCTGGTTTTGTGCGCAGTCCAACTCTTGCTAATGAGAACATC -ATGGGCCTTGTGTGAAGCTTTAACTCTAGCTACAGGACCAATAACAACACTCTGGGAAGG -ATCACCTGGTAAGTTCTGGAACACCACGATAGCTGTTTCCATGGCGAACATTTTTAGAGG -GAGCTATTTAGCAGGAGCTGGGCTTGCTTTTTCTATTATGAAATCAGTTGGAACAGGAAA -AAGAGGAACAGGCTCACAAGGTGAAACTTTAGGAGAAAAATGGAAAAAGAAATTAAATCA -ATTATCCCGGAAAGAGTTTGACCTTTACAAGAAATCTGGAATCACTGAAGTGGATAGAAC -AGAAGCCAAAGAAGGGTTGAAAAGAGGAGAGACAACACATCATGCCGTGTCCCGAGGTAG -CGCAAAACTTCAATGGTTTGTGGAAAGAAACATGGTCGTTCCCGAAGGAAGAGTCATAGA -CTTGGGCTGTGGAAGAGGAGGCTGGTCATATTACTGTGCAGGACTGAAAAAAGTCACAGA -AGTGCGAGGATACACAAAAGGCGGTCCAGGACACGAAGAACCAGTACCTATGTCTACATA -TGGATGGAACATAGTTAAGTTAATGAGCGGAAAGGATGTGTTCTATCTCCCACCTGAAAA -GTGTGATACCCTGTTGTGTGACATTGGAGAATCTTCACCAAGCCCAACAGTGGAAGAGAG -CAGAACTATAAGAGTTTTGAAGATGGTTGAACCATGGCTAAAAAACAACCAGTTTTGCAT -TAAAGTTTTGAACCCTTACATGCCAACTGTGATTGAGCACCTAGAAAGACTACAAAGGAA -ACATGGAGGAATGCTTGTGAGAAATCCACTTTCACGAAACTCCACGCACGAAATGTACTG -GATATCTAATGGCACAGGTAACATTGTCTCTTCAGTCAACATGGTGTCTAGATTGCTACT -GAACAGGTTCACGATGACACACAGGAGACCCACCATAGAGAAAGATGTGGATTTAGGAGC -AGGAACTCGACATGTTAATGCGGAACCAGAAACACCCAACATGGATGTCATTGGGGAAAG -AATAAAAAGGATCAAGGAGGAGCATAATTCAACATGGCACTATGATGACGAAAACCCCTA -CAAAACGTGGGCTTACCATGGATCCTATGAAGTCAAAGCCACAGGCTCAGCCTCCTCCAT -GATAAATGGAGTCGTGAAACTCCTCACCAAACCATGGGATGTGGTGCCCATGGTGACACA -GATGGCAATGACAGACACAACTCCATTTGGCCAGCAGAGAGTCTTTAAAGAGAAAGTGGA -CACCAGGACGCCCAGGCCCATGCCAGGGACAAGAAAGGCTATGGAGATCACAGCGGAGTG -GCTCTGGAGAACCCTGGGAAGGAACAAAAGACCCAGATTATGCACAAGGGAAGAGTTTAC -AAAAAAGGTCAGAACTAACGCAGCCATGGGCGCCGTTTTCACAGAGGAGAACCAATGGGA -CAGTGCGAAAGCTGCTGTTGAGGATGAAGAATTTTGGAAACTTGTGGACAGAGAACGTGA -ACTCCACAAATTGGGCAAATGTGGAAGCTGCGTTTATAACATGATGGGCAAGAGAGAGAA -AAAACTTGGAGAGTTTGGCAAAGCAAAAGGCAGTAGAGCTATATGGTACATGTGGTTGGG -AGCCAGGTACCTTGAGTTCGAAGCCCTTGGATTCTTAAATGAAGACCACTGGTTCTCGCG -TGAAAACTCTTACAGTGGAGTAGAAGGAGAAGGACTGCACAAGCTAGGCTACATATTAAG -GGACATTTCCAAGATACCCGGAGGAGCCATGTATGCTGATGACACAGCTGGTTGGGACAC -AAGAATAACAGAAGATGACCTGCACAATGAGGAAAAGATCATACAGCAAATGGACCCTGA -ACACAGGCAGTTAGCGAACGCTATATTCAAGCTCACATACCAAAACAAAGTGGTCAAAGT -TCAACGACCGACTCCAACGGGCACGGTAATGGATATTATATCTAGGAAAGACCAAAGGGG -CAGTGGACAACTGGGAACTTATGGCCTGAATACATTCACCAACATGGAAGCCCAGTTAGT -CAGACAAATGGAAGGAGAAGGTGTGCTGACAAAGGCAGACCTCGAGAACCCTCATCTGCT -AGAGAAGAAAATCACACAATGGTTGGAAACCAAAGGAGTGGAGAGGTTAAAAAGAATGGC -CATTAGCGGGGATGATTGCGTGGTGAAACCAATCGATGACAGGTTCGCTAATGCCCTGCT -TGCTTTGAACGATATGGGAAAGGTTCGGAAAGACATACCTCAATGGCAGCCATCAAAGGG -ATGGCATGATTGGCAACAGGTTCCTTTCTGCTCCCACCACTTTCATGAATTGATCATGAA -AGATGGAAGAAAGTTGGTGGTTCCCTGCAGACCCCAGGACGAACTAATAGGAAGAGCAAG -AATCTCTCAAGGAGCGGGATGGAGCCTTAGAGAAACTGCATGTCTGGGGAAAGCCTACGC -CCAAATGTGGAGTCTCATGTATTTTCACAGAAGAGATCTCAGATTAGCATCCAACGCCAT -ATGTTCAGCAGTACCAGTCCACTGGGTTCCCACAAGTAGAACGACATGGTCTATTCATGC -TCACCATCAGTGGATGACTACAGAAGACATGCTTACTGTTTGGAACAGGGTGTGGATAGA -GGAAAATCCATGGATGGAAGACAAAACTCCAGTTACAACTTGGGAAAATGTTCCATATCT -AGGAAAGAGAGAAGACCAATGGTGTGGATCACTTATTGGTCTCACTTCCAGAGCAACCTG -GGCCCAGAACATACCCACAGCAATTCAACAGGTGAGAAGCCTTATAGGCAATGAAGAGTT -CCTGGACTACATGCCTTCAATGAAGAGATTCAGGAAGGAAGAGGAGTCGGAGGGAGCCAT -TTGGTAAACGTAGGAAGTGGAAAAGAGGCTAACTGTCAGGCCACCTTAAGCCACAGTACG -GAAGAAGCTGTGCTGCCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGAAGTCAGGCCCC -AAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGTCGTGGGGACGTAAAACCTG -GGAGGCTGCAAACTGTGGAAGCTGTACGCACGGTGTAGCAGACTAGCGGTTAGAGGAGAC -CCCTCCCATGACACAACGCAGCAGCGGGGCCCGAGCACTGAGGGAAGCTGTACCTCCTTG -CAAAGGACTAGAGGTTAGAGGAGACCCCCCGCAAATAAAAACAGCATATTGACGCTGGGA -GAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGG -AATGGTGCTGTTGAATCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome +AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGACTCGGAAGCTTGCTTAACGTAGTGCTGACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGAAAACCGTCTATCAATATGCTGAAACGCGTGAGAAACCGTGTGTCAACTGGATCACAGTTGGCGAAGAGATTCTCAAGAGGATTGCTGAACGGCCAAGGACCAATGAAATTGGTTATGGCGTTCATAGCTTTCCTCAGATTTCTAGCCATTCCACCGACAGCAGGAGTCTTGGCTAGATGGGGTACCTTCAAGAAGTCGGGGGCTATTAAGGTCCTAAAAGGCTTCAAGAAGGAGATCTCAAACATGCTGAGCATTATCAACAAACGGAAAAAGACATCGCTCTGTCTCATGATGATGTTACCAGCAACACTTGCTTTCCACTTGACTTCACGAGATGGAGAGCCGCGCATGATTGTGGGGAAGAATGAAAGAGGAAAATCCCTACTTTTTAAGACAGCCTCTGGAATCAACATGTGCACACTCATAGCCATGGATTTGGGAGAGATGTGTGATGACACGGTCACTTACAAATGCCCCCACATTACCGAAGTGGAGCCTGAAGACATTGACTGCTGGTGCAACCTTACATCGACATGGGTGACTTATGGAACGTGCAATCAAGCTGGAGAGCATAGACGCGATAAGAGATCAGTGGCGTTAGCTCCCCATGTCGGCATGGGACTGGACACACGCACCCAAACCTGGATGTCGGCTGAAGGAGCTTGGAGACAAGTCGAGAAGGTAGAGACATGGGCCCTTAGGCACCCAGGGTTCACCATACTAGCCCTATTTCTTGCCCATTACATAGGCACTTCCTTGACCCAGAAAGTGGTTATTTTTATACTACTAATGCTGGTCACCCCATCCATGACAATGAGATGTGTGGGAGTAGGAAACAGAGATTTTGTGGAAGGCCTATCGGGAGCTACGTGGGTTGACGTGGTGCTCGAGCACGGTGGGTGTGTGACTACCATGGCTAAGAACAAGCCCACGCTGGATATAGAGCTTCAGAAGACCGAGGCCACCCAACTGGCGACCCTAAGGAAGCTATGCATTGAGGGAAAAATTACCAACATAACAACCGACTCAAGGTGTCCCACCCAAGGGGAAGCGATTTTACCTGAGGAGCAGGACCAGAACTACGTGTGTAAGCATACATACGTGGACAGAGGCTGGGGAAACGGTTGTGGTTTGTTTGGCAAGGGAAGCTTGGTGACATGCGCGAAATTTCAATGTTTAGAATCAATAGAGGGAAAAGTGGTGCAACATGAGAACCTCAAATACACCGTCATCATCACAGTGCACACAGGAGACCAACACCAGGTGGGAAATGAAACGCAGGGAGTCACGGCTGAGATAACACCCCAGGCATCAACCGCTGAAGCCATCTTACCTGAATATGGAACCCTTGGGCTAGAATGCTCACCACGGACAGGTTTGGATTTCAATGAAATGATCTTATTGACAATGAAGAACAAAGCATGGATGGTACATAGACAATGGTTCTTTGACCTACCTCTACCATGGACATCAGGAGCTACAACAGAAACACCAACCTGGAACAGGAAAGAGCTTCTTGTGACATTCAAAAACGCACATGCAAAAAAACAAGAAGTAGTTGTCCTTGGATCGCAAGAGGGAGCAATGCATACAGCACTGACAGGAGCTACAGAGATCCAAACCTCAGGAGGCACAAGCATTTTTGCGGGGCACTTAAAATGTAGACTCAAGATGGACAAATTGGAACTCAAGGGGATGAGCTATGCAATGTGCTTGAATACCTTTGTGTTGAAGAAAGAAGTCTCCGAAACGCAGCATGGGACAATACTCATTAAGGTTGAGTACAAAGGGGAAGATGCACCCTGCAAGATTCCTTTCTCCACGGAGGATGGACAAGGGAAAGCTCACAATGGCAGACTGATCACAGCCAACCCAGTGGTGACCAAGAAGGAGGAGCCTGTCAATATTGAGGCTGAACCTCCTTTTGGGGAAAGTAATATAGTAATTGGAATTGGAGACAAAGCCTTGAAAATCAACTGGTACAAGAAGGGAAGCTCGATTGGGAAGATGTTCGAGGCCACTGCCAGAGGTGCAAGGCGCATGGCCATCTTGGGAGACACAGCCTGGGACTTTGGATCAGTGGGTGGTGTTTTGAATTCATTAGGGAAAATGGTGCACCAAATATTTGGAAGTGCTTACACAGCCCTATTTAGTGGAGTCTCCTGGATAATGAAAATTGGAATAGGTGTCCTCTTAACCTGGATAGGGTTGAATTCAAAAAACACTTCTATGTCATTTTCATGCATTGCGATAGGAATCATTACACTCTATCTGGGAGCCGTGGTGCAAGCTGACATGGGGTGTGTCATAAACTGGAAAGGCAAAGAACTCAAATGTGGAAGTGGAATTTTCGTCACTAATGAGGTCCACACCTGGACAGAGCAATACAAATTTCAAGCAGACTCCCCCAAAAGACTGGCGACAGCCATTGCAGGCGCTTGGGAGAATGGAGTGTGCGGAATCAGGTCAACAACCAGAATGGAGAACCTCTTGTGGAAGCAAATAGCCAATGAACTGAACTACATATTATGGGAAAACAACATCAAATTAACGGTAGTTGTGGGCGACATAATTGGGGTCTTAGAGCAAGGGAAAAGAACACTAACACCACAACCCATGGAGCTAAAATATTCATGGAAAACATGGGGAAAGGCAAAAATAGTGACAGCTGAAACACAAAATTCCTCTTTCATAATAGATGGGCCAAACACACCGGAGTGTCCAAGTGCCTCAAGAGCATGGAATGTGTGGGAGGTGGAAGATTACGGGTTCGGAGTCTTCACAACCAACATATGGCTGAAACTCCGAGAGGTGTACACCCAACTATGTGACCATAGGCTAATGTCGGCAGCCGTCAAGGATGAGAGGGCCGTACACGCCGACATGGGCTATTGGATAGAAAGCCAAAAGAATGGAAGTTGGAAGCTAGAAAAAGCATCCCTCATAGAGGTGAAAACCTGCACATGGCCAAAATCACACACTCTTTGGAGCAATGGTGTGCTAGAGAGTGACATGATCATCCCAAAGAGTCTAGCTGGTCCTATTTCGCAACACAACCACAGGCCCGGGTACCACACCCAAACGGCAGGACCCTGGCACTTAGGAAAATTGGAGCTGGACTTCAACTATTGTGAAGGAACAACAGTTGTCATCACAGAAAACTGTGGGACAAGAGGCCCATCATTGAGAACAACAACAGTGTCAGGGAAGTTGATACACGAATGGTGTTGCCGCTCGTGCACACTTCCTCCCCTGCGATACATGGGAGAAGACGGCTGCTGGTATGGCATGGAAATTAGACCCATTAATGAGAAAGAAGAGAACATGGTAAAGTCTTTAGCCTCAGCAGGGAGTGGAAAGGTGGACAACTTCACAATGGGTGTCTTGTGTTTGGCAATCCTCTTTGAAGAGGTGATGAGAGGAAAATTTGGGAAAAAACACATGATTGCAGGGGTTCTCTTCACGTTTGTGCTCCTTCTCTCAGGGCAAATAACATGGAGAGACATGGCGCACACACTCATAATGATTGGGTCCAACGCCTCTGACAGAATGGGAATGGGCGTCACTTACCTAGCTTTAATTGCAACATTTAAAATTCAGCCATTCTTGGCTTTGGGATTCTTCCTGAGGAAACTGACATCTAGAGAAAATTTATTGTTGGGAGTTGGGTTGGCCATGGCAACAACGTTACAACTGCCAGAGGACATTGAACAAATGGCGAATGGAATTGCTTTGGGGCTCATGGCTCTTAAACTGATAACACAATTTGAAACATACCAACTATGGACGGCATTAGTCTCCCTAACGTGTTCAAATACAATTTTCACGTTGACTGTTGCCTGGAGAACAGCCACCCTGATTTTGGCCGGAATTTCGCTTTTGCCAGTGTGCCAGTCTTCGAGCATGAGGAAAACAGATTGGCTCCCAATGACTGTGGCAGCTATGGGAGTTCCACCCCTACCACTTTTTATCTTCAGTTTGAAAGATACACTCAAAAGGAGAAGCTGGCCACTGAATGAGGGGGTGATGGCTGTTGGACTTGTGAGCATTCTAGCTAGTTCTCTCCTTAGGAATGATGTGCCCATGGCTGGACCATTAGTGGCTGGGGGCTTGCTGATAGCGTGCTACGTCATAACTGGCACGTCAGCAGACCTCACTGTAGAAAAAGCAGCAGATGTAACATGGGAGGAAGAGGCTGAGCAAACAGGAGTGTCCCACAATTTAATGATCACAGTTGATGATGATGGAACAATGAGAATAAAAGATGATGAGACTGAGAACATCCTAACAGTGCTTTTAAAAACAGCATTACTAATAGTATCAGGCATCTTTCCATACTCCATACCCGCAACACTGTTGGTCTGGCATACTTGGCAAAAGCAAACCCAAAGATCCGGCGTCCTATGGGACGTACCCAGCCCCCCAGAGACACAGAAAGCAGAACTGGAAGAAGGGGTCTATAGGATCAAACAGCAAGGAATTTTTGGGAAAACCCAAGTGGGGGTTGGAGTACAGAAAGAAGGAGTTTTCCACACCATGTGGCACGTCACAAGAGGGGCAGTGTTGACACACAATGGGAAAAGACTGGAACCAAACTGGGCTAGCGTGAAAAAAGATCTGATTTCATACGGAGGAGGATGGAGATTGAGTGCACAATGGCAAAAGGGAGAGGAGGTGCAGGTTATTGCCGTAGAGCCTGGGAAGAACCCAAAGAACTTTCAAACCATGCCAGGCATTTTTCAGACAACAACAGGGGAAATAGGAGCAATTGCACTGGACTTCAAGCCTGGAACTTCAGGATCTCCCATCATAAACAGAGAGGGAAAGGTAGTGGGACTGTATGGCAATGGAGTGGTTACAAAGAATGGTGGCTATGTCAGTGGAATAGCGCAAACAAATGCAGAACCAGACGGACCGACACCAGAGTTGGAAGAAGAGATGTTCAAAAAGCGAAATCTAACCATAATGGATCTTCATCCTGGGTCAGGAAAGACGCGGAAATACCTTCCAGCTATTGTTAGAGAGGCAATCAAGAGACGCTTAAGGACTCTAATTTTGGCACCAACAAGGGTGGTTGCAGCTGAGATGGAAGAAGCATTGAAAGGGCTCCCAATAAGGTATCAAACAACTGCAACAAAATCTGAACACACAGGAAGAGAGATTGTTGATCTAATGTGCCACGCAACGTTCACAATGCGCTTGCTGTCACCAGTCAGGGTTCCAAACTACAACTTGATAATAATGGATGAGGCTCATTTCACAGACCCAGCCAGTATAGCGGCTAGAGGGTACATATCAACTCGTGTAGGAATGGGAGAGGCAGCCGCAATTTTCATGACAGCAACACCCCCTGGAACAGCTGATGCCTTTCCTCAGAGCAACGCTCCAATTCAAGATGAAGAAAGGGACATACCGGAACGCTCATGGAATTCAGGCAATGAATGGATTACCGACTTTGTTGGGAAGACGGTGTGGTTTGTCCCTAGCATCAAAGCCGGAAATGACATAGCAAACTGCTTGCGGAAAAACGGAAAAAAGGTCATTCAACTTAGTAGGAAGACTTTTGACACAGAATATCAAAAGACTAAACTGAATGATTGGGACTTTGTGGTGACAACAGACATTTCAGAAATGGGAGCCAATTTCAAAGCAGATAGAGTGATCGACCCAAGAAGATGTCTCAAGCCAGTGATTTTGACAGATGGACCCGAGCGGGTGATCCTGGCTGGACCAATGCCAGTCACCGTAGCGAGCGCTGCGCAAAGGAGAGGGAGAGTTGGCAGGAACCCACAAAAAGAAAATGACCAGTACATATTCACGGGCCAGCCTCTCAACAATGATGAAGACCATGCTCACTGGACAGAAGCAAAAATGCTGCTGGACAACATCAACACACCAGAAGGGATTATACCAGCTCTCTTTGAACCAGAAAGGGAGAAGTCAGCCGCCATAGACGGCGAATACCGCCTGAAGGGTGAGTCCAGGAAGACCTTCGTGGAACTCATGAGGAGGGGTGACCTCCCAGTTTGGCTAGCCCATAAAGTAGCATCAGAAGGGATCAAATATACAGATAGAAAATGGTGCTTTGATGGAGAACGTAATAATCAAATTTTAGAGGAGAATATGGATGTGGAAATCTGGACAAAGGAAGGAGAAAAGAAAAAATTGAGACCTAGGTGGCTTGATGCCCGCACTTATTCAGATCCCTTAGCACTCAAGGAATTCAAGGATTTTGCAGCTGGCAGAAAGTCAATCGCCCTTGATCTTGTGACAGAAATAGGAAGAGTGCCTTCACACTTAGCCCACAGAACGAGAAACGCCCTGGACAATTTGGTGATGCTGCACACGTCAGAACATGGCGGTAGGGCCTACAGGCATGCAGTGGAGGAACTACCAGAAACAATGGAAACACTCTTACTCCTGGGACTCATGATCTTGTTAACAGGTGGAGCAATGCTTTTCTTGATATCAGGTAAAGGGATTGGAAAGACTTCAATAGGACTCATTTGTGTAATTGCTTCCAGCGGCATGTTATGGATGGCTGATGTCCCACTCCAATGGATCGCGTCGGCTATAGTCCTGGAGTTTTTTATGATGGTGTTGCTCATACCAGAACCAGAAAAGCAGAGAACTCCCCAAGACAACCAACTCGCATATGTCGTGATAGGCATACTTACATTGGCTGCAATAGTAGCAGCCAATGAAATGGGACTGTTGGAAACTACAAAGAGAGATTTAGGAATGTCTAAAGAACCAGGTGTTGTTTCTCCAACCAGCTATTTGGATGTGGACTTGCACCCAGCATCAGCCTGGACATTGTACGCCGTGGCCACAACAGTAATAACACCAATGTTGAGACATACCATAGAGAATTCCACAGCAAATGTGTCCCTGGCAGCTATAGCTAACCAGGCAGTGGTCCTGATGGGTTTAGACAAAGGATGGCCGATATCGAAAATGGACTTAGGCGTACCACTACTGGCACTGGGTTGCTATTCACAAGTGAACCCACTAACTCTCACAGCGGCAGTACTTTTGCTAGTCACACATTATGCTATTATAGGTCCAGGATTGCAGGCAAAAGCCACTCGTGAAGCTCAGAAAAGGACAGCTGCTGGAATAATGAAGAATCCAACGGTGGATGGGATAATGACAATAGACCTAGATCCTGTAATATACGATTCAAAATTTGAAAAGCAACTAGGACAGGTTATGCTCCTGGTTCTGTGTGCAGTTCAACTTTTGTTAATGAGAACATCATGGGCCTTGTGTGAAGCTCTAACCCTAGCCACAGGACCAATAACAACACTCTGGGAAGGATCACCTGGGAAGTTTTGGAACACCACGATAGCTGTTTCCATGGCGAACATCTTTAGAGGGAGCTATTTAGCAGGAGCTGGGCTTGCTTTTTCTATCATGAAATCAGTTGGAACAGGAAAGAGAGGAACAGGGTCACAAGGTGAAACCTTAGGAGAAAAGTGGAAAAAGAAATTAAATCAGTTATCCCGGAAAGAGTTTGACCTTTACAAGAAATCCGGAATCACTGAAGTGGATAGAACAGAAGCCAAAGAAGGGTTGAAAAGAGGAGAAATAACACACCATGCCGTGTCCAGAGGCAGCGCAAAACTTCAATGGTTCGTGGAGAGAAACATGGTCATTCCCGAAGGAAGAGTCATAGACTTAGGCTGTGGAAGAGGAGGCTGGTCATATTACTGTGCAGGACTGAAAAAAGTTACAGAAGTGCGAGGATACACAAAAGGCGGCCCAGGACACGAAGAACCAGTACCTATGTCTACATACGGATGGAACATAGTCAAGTTAATGAGTGGAAAGGATGTGTTTTATCTTCCACCTGAAAAGTGTGATACCCTATTGTGTGACATTGGAGAATCTTCACCAAGCCCAACAGTGGAAGAAAGCAGAACCATAAGAGTCTTGAAGATGGTTGAACCATGGCTAAAAAACAACCAGTTTTGCATTAAAGTATTGAACCCTTACATGCCAACTGTGATTGAGCACCTAGAAAGACTACAAAGGAAACATGGAGGAATGCTTGTGAGAAATCCACTCTCACGAAACTCCACGCACGAAATGTACTGGATATCCAATGGTACAGGCAACATCGTCTCTTCAGTCAACATGGTATCCAGATTGCTACTGAACAGATTCACAATGACACACAGGAGACCCACCATAGAGAAAGATGTGGATTTAGGAGCAGGAACCCGACATGTCAATGCGGAACCAGAAACACCCAACATGGATGTCATTGGGGAAAGAATAAAAAGGATCAAGGAGGAGCATAGTTCAACATGGCACTATGATGATGAAAATCCTTACAAAACGTGGGCTTACCATGGATCCTATGAAGTCAAAGCCACAGGCTCAGCCTCCTCCATGATAAATGGAGTCGTGAAACTCCTCACAAAACCATGGGATGTGGTGCCCATGGTGACACAGATGGCAATGACAGATACAACCCCATTTGGCCAGCAAAGAGTTTTTAAAGAGAAAGTGGACACCAGGACACCCAGGCCCATGCCAGGAACAAGAAAGGTTATGGAGATCACAGCGGAGTGGCTTTGGAGAACCCTGGGAAGGAACAAAAGACCCAGATTATGCACAAGGGAGGAGTTCACAAAAAAGGTCAGAACCAACGCAGCTATGGGCGCCGTTTTCACAGAGGAGAACCAATGGGACAGTGCGAGAGCTGCTGTTGAGGACGAAGAATTTTGGAAACTTGTGGACAGAGAACGTGAACTCCACAAATTGGGCAAGTGTGGAAGCTGCGTTTACAACATGATGGGCAAGAGAGAGAAGAAACTTGGAGAGTTTGGCAAAGCAAAAGGCAGTAGAGCTATATGGTACATGTGGTTGGGAGCCAGGTACCTTGAGTTCGAGGCACTCGGATTCTTAAATGAAGACCACTGGTTCTCGCGTGAAAACTCTTACAGTGGAGTAGAAGGAGAAGGACTGCACAAGCTGGGATACATCTTAAGAGATATTTCCAAGATACCCGGAGGAGCTATGTATGCTGATGACACAGCTGGTTGGGACACAAGAATAACAGAAGATGACCTGCACAATGAGGAAAAAATCACACAGCAAATGGACCCTGAACACAGGCAGTTAGCGAACGCTATATTCAAGCTCACATACCAAAACAAAGTGGTCAAAGTTCAACGACCAACTCCAAAGGGCACGGTAATGGACATCATATCTAGGAAAGACCAAAGAGGCAGTGGACAGGTGGGAACTTATGGTCTGAATACATTCACCAACATGGAAGCCCAGTTAATCAGACAAATGGAAGGAGAAGGTGTGTTGTCAAAGGCAGACCTCGAGAACCCTCATCTGCTAGAGAAGAAAATTACACAATGGTTGGAAACCAAAGGAGTGGAGAGGTTAAAAAGAATGGCCATCAGCGGGGATGATTGCGTAGTGAAACCAATCGATGACAGGTTCGCCAATGCCCTGCTTGCCCTGAACGATATGGGAAAGGTTAGGAAGGACATACCTCAATGGCAGCCATCAAAGGGATGGCATGATTGGCAACAGGTCCCTTTCTGCTCCCACCACTTTCATGAATTGATCATGAAAGATGGAAGAAAGTTGGTAGTTCCCTGCAGACCCCAGGACGAACTAATAGGAAGAGCGAGAATCTCTCAAGGAGCAGGATGGAGCCTTAGAGAAACTGCATGTCTAGGGAAAGCCTACGCTCAAATGTGGACTCTCATGTATTTTCACAGAAGAGATCTTAGACTAGCATCCAACGCCATATGTTCAGCAGTACCAGTCCATTGGGTCCCCACAAGCAGAACGACATGGTCTATTCATGCTCACCATCAGTGGATGACTACAGAAGACATGCTTACTGTCTGGAACAGGGTGTGGATAGAGGACAATCCATGGATGGAAGACAAAACTCCAGTCACAACTTGGGAAGATGTTCCATATCTAGGGAAGAGAGAAGACCAATGGTGCGGATCACTCATTGGTCTCACTTCCAGAGCAACCTGGGCCCAGAACATACTCACAGCAATCCAACAGGTGAGAAGCCTTATAGGCAATGAAGAGTTTCTGGACTACATGCCTTCGATGAAGAGATTCAGGAAGGAGGAGGAGTCAGAGGGAGCCATTTGGTAAACGCAGGAAGTGAAAAAGAGGCAAACTGTCAGGCCACCTTAAGCCACAGTACGGAAGAAGCTGTGCAGCCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGAAGTCAGGCCCAAAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGTCGTGGGGACGTAAAGCCTGGGAGGCTGCAAACCGTGGAAGCTGTACGCACGGTGTAGCAGACTAGCGGTTAGAGGAGACCCCTCCCATGACACAACGCAGCAGCGGGGCCCGAGCACTGAGGGAAGCTGTACCTCCTTGCAAAGGACTAGAGGTTAGAGGAGACCCCCCGCAAATAAAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/datasets/denv3/tree.json b/nextclade/datasets/denv3/tree.json index a2b90bdd..bd620d44 100644 --- a/nextclade/datasets/denv3/tree.json +++ b/nextclade/datasets/denv3/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Real-time tracking of dengue virus evolution", "updated": "2024-05-25", "build_url": "https://github.com/nextstrain/dengue", "maintainers": [{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": true, "color_by": "clade_membership"}, "genome_annotations": {"nuc": {"end": 10707, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/config/reference_denv3_genome.gb"}, "2K": {"end": 6820, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 6752, "strand": "+", "type": "CDS"}, "C": {"end": 436, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 95, "strand": "+", "type": "CDS"}, "E": {"end": 2413, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 935, "strand": "+", "type": "CDS"}, "M": {"end": 934, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 437, "strand": "+", "type": "CDS"}, "NS1": {"end": 3469, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 2414, "strand": "+", "type": "CDS"}, "NS2A": {"end": 4123, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 3470, "strand": "+", "type": "CDS"}, "NS2B": {"end": 4513, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 4124, "strand": "+", "type": "CDS"}, "NS3": {"end": 6370, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 4514, "strand": "+", "type": "CDS"}, "NS4A": {"end": 6751, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 6371, "strand": "+", "type": "CDS"}, "NS4B": {"end": 7564, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 6821, "strand": "+", "type": "CDS"}, "NS5": {"end": 10264, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 7565, "strand": "+", "type": "CDS"}, "pr": {"end": 709, "seqid": "../phylogenetic/config/reference_denv3_genome.gb", "start": 437, "strand": "+", "type": "CDS"}}, "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Israel", "#5E1D9D"], ["Saudi Arabia", "#571EA3"], ["Pakistan", "#4D22AE"], ["Maldives", "#4A27B2"], ["India", "#472CB7"], ["Sri Lanka", "#4531BC"], ["Nepal", "#4236C0"], ["Bangladesh", "#403BC5"], ["Myanmar", "#4041C7"], ["Thailand", "#3F47C9"], ["Malaysia", "#3F4DCB"], ["Laos", "#3F53CD"], ["Singapore", "#3E59CF"], ["China", "#3F5FD0"], ["Cambodia", "#4064CF"], ["Vietnam", "#416ACF"], ["Indonesia", "#4270CE"], ["Taiwan", "#447BCD"], ["Philippines", "#457FCA"], ["French Polynesia", "#4C91BF"], ["Australia", "#4E95BC"], ["Papua New Guinea", "#5199B8"], ["Fiji", "#58A2AC"], ["Senegal", "#5AA5A7"], ["Burkina Faso", "#60AA9E"], ["Niger", "#70B487"], ["Gabon", "#74B583"], ["Angola", "#7BB77A"], ["Mozambique", "#82BA71"], ["Kenya", "#8BBB6A"], ["Ethiopia", "#8FBC66"], ["Somalia", "#A0BE58"], ["United Kingdom", "#A9BD53"], ["France", "#ADBD50"], ["Italy", "#B5BD4C"], ["Paraguay", "#C5B945"], ["Bolivia", "#C9B843"], ["Brazil", "#CDB642"], ["Peru", "#D0B441"], ["Ecuador", "#D3B240"], ["Colombia", "#D6B03F"], ["Guyana", "#DCAB3C"], ["Venezuela", "#DEA73B"], ["Trinidad and Tobago", "#E0A33B"], ["Grenada", "#E59838"], ["Nicaragua", "#E69337"], ["Barbados", "#E68835"], ["Saint Lucia", "#E67C33"], ["Guadeloupe", "#E3622D"], ["Saint Kitts and Nevis", "#E04C29"], ["Jamaica", "#DF4528"], ["Dominican Republic", "#DE3E27"], ["Mexico", "#DD3625"], ["Cuba", "#DC2F24"], ["USA", "#DB2823"]]}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["Asia", "#447CCD"], ["Oceania", "#5EA9A1"], ["Africa", "#8ABB6A"], ["Europe", 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America", "confidence": {"North America": 0.9999999999999999}, "entropy": -9.99866855976916e-13}, "clade_membership": {"value": "DENV3/III"}, "serotype_genbank": {"value": "denv3"}, "country": {"value": "Nicaragua", "confidence": {"Nicaragua": 1.0}, "entropy": -1.000088900581841e-12}, "genotype_nextclade": {"value": "DENV3/III", "confidence": {"DENV3/III": 1.0}, "entropy": -1.000088900581841e-12}}, "branch_attrs": {"mutations": {"nuc": ["C11T", "T14A", "A15G", "G17T", "A25G", "A29C", "C30A", "A5749G"]}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}, "root_sequence": {"nuc": "AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGACTCGGAAGCTTGCTTAACGTAGTGCTGACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAGAAGACGGGAAAACCGTCTATCAATATGCTGAAACGCGTGAGAAACCGTGTGTCAACTGGATCACAGTTGGCGAAGAGATTCTCAAAAGGACTGCTGAACGGCCAGGGACCAATGAAATTGGTTATGGCGTTCATAGCTTTCCTCAGATTTCTAGCCATTCCACCAACAGCAGGAGTCTTGGCTAGATGGGGAACCTTCAAGAAGTCGGGGGCCATTAAGGTCCTGAAAGGCTTCAAGAAGGAGATCTCAAACATGCTGAGCATAATCAACCAACGGAAAAAGACATCGCTCTGTCTCATGATGATATTGCCAGCAGCACTTGCTTTCCACTTGACTTCACGAGATGGAGAGCCGCGCATGATTGTGGGGAAGAATGAAAGAGGTAAATCCCTACTTTTTAAGACAGCCTCTGGAATCAACATGTGCACACTCATAGCCATGGATTTGGGAGAGATGTGTGATGACACGGTCACTTACAAATGCCCCCACATTACCGAAGTGGAACCTGAAGACATTGACTGCTGGTGCAACCTTACATCAACATGGGTGACTTATGGAACGTGCAATCAAGCTGGAGAGCATAGACGCGACAAGAGATCAGTGGCGTTAGCTCCCCATGTCGGCATGGGACTGGACACACGCACCCAAACCTGGATGTCGGCTGAAGGAGCTTGGAGACAAGTCGAGAAGGTAGAGACATGGGCCCTTAGGCACCCAGGGTTCACCATACTAGCCCTATTTCTCGCCCATTACATAGGCACTTCCCTGACCCAGAAGGTGGTTATTTTCATATTATTAATGCTGGTCACCCCATCCATGACAATGAGATGTGTGGGAGTAGGAAACAGAGATTTTGTGGAAGGGCTATCAGGAGCTACGTGGGTTGACGTGGTGCTCGAGCACGGGGGGTGTGTGACTACCATGGCTAAGAACAAGCCCACGCTGGATATAGAGCTTCAGAAGACCGAGGCCACCCAACTGGCGACCCTAAGGAAGCTATGCATTGAGGGGAAAATTACCAACATAACAACTGACTCAAGATGTCCTACCCAAGGGGAAGCGGTTTTGCCTGAGGAGCAGGACCAGAACTACGTGTGTAAGCATACATACGTAGACAGAGGTTGGGGGAACGGTTGTGGTTTGTTTGGCAAAGGAAGCTTGGTAACATGTGCGAAATTTCAATGCCTGGAACCAATAGAGGGAAAAGTGGTGCAATATGAGAACCTCAAATACACCGTCATCATTACAGTGCACACAGGAGACCAACACCAGGTGGGAAATGAAACGCAAGGAGTCACGGCTGAGATAACACCTCAGGCATCAACCACTGAAGCCATCTTGCCTGAATATGGAACCCTTGGGCTAGAATGCTCACCACGGACAGGTTTGGATTTCAATGAAATGATCTTACTAACAATGAAGAACAAAGCATGGATGGTACATAGACAATGGTTCTTTGACCTACCTCTACCATGGGCATCAGGAGCTACAACAGAAACACCAACCTGGAACAGGAAGGAGCTTCTTGTGACATTCAAAAACGCACATGCGAAAAAACAAGAAGTAGTTGTCCTTGGATCGCAAGAGGGAGCAATGCATACCGCACTGACAGGAGCTACAGAAATCCAAAACTCAGGAGGCACAAGCATTTTCGCGGGGCACTTAAAATGTAGACTTAAGATGGACAAATTGGAACTCAAGGGGATGAGCTATGCAATGTGCACGAATACCTTTGTGTTGAAGAAAGAAGTCTCAGAAACGCAGCACGGGACAATACTCATTAAGGTTGAGTACAAAGGGGAAGATGCACCTTGCAAGATTCCCTTTTCCACAGAGGATGGACAAGGGAAAGCTCATAATGGCAGACTGATCACAGCCAACCCTGTGGTGACTAAGAAGGAGGAGCCTGTCAATATTGAGGCTGAACCTCCTTTTGGGGAAAGCAATATAGTAATTGGAATTGGAGACAACGCCTTGAAAATCAACTGGTACAAGAAGGGGAGCTCGATTGGGAAGATGTTCGAGGCCACTGAAAGGGGTGCAAGGCGCATGGCCATCTTGGGAGACACAGCTTGGGACTTTGGATCAGTGGGTGGTGTTCTGAACTCATTAGGCAAAATGGTGCACCAAATATTTGGAAGTGCTTATACAGCCCTGTTCAGTGGAGTCTCTTGGGTGATGAAAATTGGAATAGGTGTCCTCTTGACTTGGATAGGGTTGAATTCAAAAAACACATCCATGTCATTTTCATGCATTGCGATAGGAATCATTACACTCTATCTGGGAGCTGTGGTACAAGCTGACATGGGGTGTGTCATAAACTGGAAGGGCAAAGAACTCAAATGTGGAAGCGGAATTTTCGTCACCAATGAGGTCCATACCTGGACAGAGCAATACAAATTCCAAGCAGACTCCCCAAAAAGATTGGCAACAGCCATTGCAGGCGCCTGGGAGAATGGAGTGTGTGGAATTAGGTCAACAACCAGAATGGAGAATCTCTTGTGGAAGCAAATAGCCAATGAACTGAACTACATATTATGGGAAAACAATATCAAATTAACGGTAGTTGTGGGCGATACACTTGGGGTCTTAGAGCAAGGGAAAAGAACACTAACACCACAACCCATGGAGCTAAAATACTCATGGAAAACGTGGGGAAAGGCAAAAATAGTGACAGCTGAAACACAAAATTCCTCTTTCATAATAGACGGGCCAAACACACCGGAGTGTCCAAGTGCCTCAAGAGCATGGAATGTGTGGGAGGTGGAAGATTACGGGTTCGGAGTCTTCACAACCAACATATGGCTGAAACTCCGAGAGGTCTACACCCAACTATGTGACCATAGGCTAATGTCGGCAGCTGTCAAGGATGAGAGGGCCGTGCATGCCGACATGGGCTACTGGATAGAAAGCCAAAAGAATGGAAGTTGGAAGCTAGAAAAAGCATCCCTCATAGAGGTAAAAACCTGCACATGGCCAAAATCACACACTCTCTGGACTAATGGTGTGCTAGAGAGTGACATGATCATCCCAAAGAGTCTAGCTGGTCCTATCTCACAACACAACTACAGGCCCGGGTACCACACCCAAACGGCAGGACCCTGGCACTTAGGAAAATTGGAGCTGGACTTCAACTACTGTGAAGGAACAACAGTTGTCATCACAGAAAGCTGTGGGACAAGAGGCCCATCATTGAGAACAACAACAGTGTCAGGGAAGTTGATACACGAATGGTGTTGCCGCTCGTGCACACTTCCCCCCCTGCGATACATGGGAGAAGACGGCTGCTGGTATGGCATGGAAATCAGACCCATCAGTGAGAAAGAAGAGAACATGGTAAAGTCTTTAGTCTCAGCGGGAAGTGGAAAGGTGGACAACTTCACAATGGGTGTCTTGTGTTTGGCAATCCTCTTTGAAGAGGTGTTGAGAGGAAAATTTGGGAAGAAACACATGATTGCAGGGGTTTTCTTTACGTTTGTGCTCCTTCTCTCAGGGCAAATAACATGGAGAGACATGGCGCACACACTAATAATGATCGGGTCCAACGCCTCTGACAGGATGGGAATGGGCGTCACCTACCTAGCTCTAATTGCAACATTTAAAATCCAGCCATTCTTGGCTTTGGGATTTTTCCTAAGAAAGCTGACATCTAGAGAAAATTTATTGTTAGGAGTTGGGTTGGCCATGGCAACAACGTTACAACTGCCAGAGGACATTGAACAAATGGCAAATGGAGTCGCTCTGGGGCTCATGGCTCTTAAACTGATAACACAATTTGAAACATACCAATTGTGGACGGCATTAGTCTCCTTAACGTGTTCAAACACAATTTTTACGTTGACTGTTGCCTGGAGAACAGCCACTCTGATTTTGGCCGGAGTTTCGCTTTTACCAGTGTGCCAGTCTTCAAGCATGAGGAAAACAGATTGGCTCCCAATGACAGTGGCAGCTATGGGAGTTCCACCCCTTCCACTTTTTATTTTTAGCTTGAAAGACACACTCAAAAGGAGAAGCTGGCCACTGAATGAAGGGGTGATGGCTGTTGGGCTTGTGAGCATTCTGGCCAGTTCTCTCCTTAGAAATGATGTGCCCATGGCTGGACCATTAGTGGCCGGGGGCTTGCTGATAGCGTGCTACGTCATAACTGGCACGTCAGCGGACCTCACTGTAGAAAAAGCCCCAGATGTAACATGGGAGGAAGAGGCTGAGCAGACAGGAGTGTCCCACAACTTAATGATCACAGTTGATGATGATGGAACAATGAGAATAAAAGATGATGAGACTGAGAACATCCTAACAGTGCTTTTAAAAACAGCATTACTAATAGTATCAGGCATTTTTCCATACTCCATACCCGCAACATTGTTGGTCTGGCACACTTGGCAAAAACAAACCCAAAGATCCGGCGTTTTATGGGACGTACCCAGCCCCCCAGAGACACAGAAAGCAGAACTGGAAGAAGGGGTTTATAGGATCAAACAGCAAGGAATTTTTGGGAAAACCCAAGTAGGGGTTGGAGTACAGAAAGAAGGAGTCTTCCACACCATGTGGCACGTCACAAGAGGGGCAGTGTTGACACATAATGGGAAAAGACTGGAACCAAACTGGGCTAGTGTGAAAAAAGATCTGATTTCATATGGAGGAGGATGGAGACTGAGCGCACAATGGCAAAAGGGGGAGGAGGTGCAGGTTATTGCCGTAGAGCCAGGGAAGAACCCAAAGAACTTTCAAACCACGCCAGGCACTTTCCAGACTACTACAGGGGAAATAGGAGCAATTGCACTGGATTTCAAGCCTGGAACTTCAGGATCTCCTATCATAAATAGAGAGGGAAAGGTAGTGGGACTGTATGGCAATGGAGTGGTTACAAAGAATGGTGGCTATGTCAGCGGAATAGCGCAAACAAATGCAGAACCAGATGGACCGACACCAGAGTTGGAAGAAGAGATGTTCAAAAAGCGAAACCTGACCATAATGGATCTTCATCCTGGGTCAGGAAAGACACGGAAATACCTTCCAGCTATTGTCAGAGAGGCAATCAAGAGACGTTTAAGAACCTTAATTTTGGCACCGACAAGGGTGGTTGCAGCTGAGATGGAAGAAGCATTGAAAGGGCTCCCAATAAGGTACCAAACAACAGCAACAAAATCTGAACACACAGGAAGAGAGATTGTTGATCTAATGTGCCACGCAACGTTCACAATGCGTTTGCTGTCACCAGTTAGGGTTCCAAATTACAACTTGATAATAATGGATGAGGCCCATTTCACAGACCCAGCCAGTATAGCGGCTAGAGGGTACATATCAACTCGTGTTGGAATGGGAGAGGCAGCCGCAATCTTCATGACAGCAACACCCCCTGGAACAGCTGATGCCTTTCCTCAGAGCAACGCTCCAATTCAAGATGAAGAAAGGGACATACCAGAACGCTCATGGAATTCAGGCAATGAATGGATTACCGACTTCGCTGGGAAAACGGTGTGGTTTGTCCCTAGCATTAAAGCCGGAAATGACATAGCAAACTGCTTGCGAAAAAACGGGAAAAAAGTCATTCAACTTAGTAGGAAGACTTTTGACACAGAATATCAGAAGACTAAACTGAATGATTGGGACTTTGTGGTGACAACTGACATTTCAGAAATGGGGGCCAATTTCAAAGCAGATAGAGTGATCGACCCAAGAAGATGTCTCAAACCAGTGATCTTGACAGATGGACCAGAGCGGGTGATCCTGGCCGGACCAATGCCAGTCACCGCGGCGAGTGCTGCGCAAAGGAGAGGGAGAGTTGGCAGGAACCCACAAAAAGAGAATGACCAGTACATATTCACGGGCCAGCCTCTCAACAATGATGAAGACCATGCTCACTGGACAGAAGCAAAAATGCTGCTGGACAACATCAACACACCAGAAGGGATTATACCAGCTCTCTTTGAACCAGAAAGGGAGAAGTCAGCCGCCATAGACGGTGAGTATCGCCTGAAGGGTGAGTCCAGGAAGACTTTCGTGGAACTCATGAGGAGGGGTGACCTTCCAGTTTGGTTAGCCCATAAAGTAGCATCAGAAGGAATCAAATACACAGATAGAAAATGGTGCTTTGATGGGCAACGCAATAATCAAATTTTAGAGGAGAACATGGATGTGGAAATTTGGACAAAGGAAGGAGAAAAGAAAAAATTGAGACCTAGGTGGCTTGATGCCCGCACTTATTCAGATCCATTGGCACTCAAGGAATTCAAGGACTTTGCGGCTGGCAGAAAGTCAATCGCCCTTGATCTTGTGACAGAAATAGGAAGAGTGCCTTCACATCTAGCCCACAGAACAAGAAACGCTCTGGACAATCTGGTGATGCTGCATACGTCAGAAGATGGCGGTAGGGCTTACAGGCATGCGGTGGAGGAACTACCAGAAACAATGGAAACACTCCTACTCTTGGGACTAATGATCTTGTTGACAGGTGGAGCAATGCTTTTCTTGATATCAGGTAAAGGGATTGGAAAGACTTCAATAGGACTCATTTGTGTAATCGCTTCCAGCGGCATGTTGTGGATGGCCGAAGTTCCACTCCAATGGATCGCGTCGGCTATAGTCCTGGAGTTTTTTATGATGGTGTTGCTCATACCAGAACCAGAAAAGCAGAGAACCCCCCAAGACAACCAACTCGCATATGTCGTGATAGGCATACTTACATTGGCTGCAACAATAGCAGCCAATGAAATGGGACTGCTGGAAACCACAAAGAGAGACTTAGGAATGTCTAAGGAGCCAGGTGTTGTTTCTCCAACCAGCTATTTGGATGTGGACTTGCACCCAGCATCAGCCTGGACATTGTACGCCGTGGCCACTACAGTAATAACACCAATGTTAAGACATACCATAGAGAATTCTACAGCAAATGTGTCCCTGGCAGCTATAGCCAACCAGGCAGTGGTCCTGATGGGTTTGGACAAAGGATGGCCAATATCAAAAATGGACTTAGGCGTGCCACTACTGGCACTGGGTTGCTATTCACAAGTGAACCCACTGACTCTAACTGCGGCAGTACTTTTGCTAATCACACATTATGCTATCATAGGTCCAGGATTGCAAGCAAAAGCCACCCGTGAAGCTCAGAAAAGGACAGCTGCTGGAATAATGAAGAATCCAACAGTGGATGGGATAATGACAATAGACCTAGATTCTGTAATATTTGATTCAAAATTTGAAAAACAACTGGGACAGGTTATGCTCCTGGTTTTGTGCGCAGTCCAACTCTTGCTAATGAGAACATCATGGGCCTTGTGTGAAGCTTTAACTCTAGCTACAGGACCAATAACAACACTCTGGGAAGGATCACCTGGTAAGTTCTGGAACACCACGATAGCTGTTTCCATGGCGAACATTTTTAGAGGGAGCTATTTAGCAGGAGCTGGGCTTGCTTTTTCTATTATGAAATCAGTTGGAACAGGAAAAAGAGGAACAGGCTCACAAGGTGAAACTTTAGGAGAAAAATGGAAAAAGAAATTAAATCAATTATCCCGGAAAGAGTTTGACCTTTACAAGAAATCTGGAATCACTGAAGTGGATAGAACAGAAGCCAAAGAAGGGTTGAAAAGAGGAGAGACAACACATCATGCCGTGTCCCGAGGTAGCGCAAAACTTCAATGGTTTGTGGAAAGAAACATGGTCGTTCCCGAAGGAAGAGTCATAGACTTGGGCTGTGGAAGAGGAGGCTGGTCATATTACTGTGCAGGACTGAAAAAAGTCACAGAAGTGCGAGGATACACAAAAGGCGGTCCAGGACACGAAGAACCAGTACCTATGTCTACATATGGATGGAACATAGTTAAGTTAATGAGCGGAAAGGATGTGTTCTATCTCCCACCTGAAAAGTGTGATACCCTGTTGTGTGACATTGGAGAATCTTCACCAAGCCCAACAGTGGAAGAGAGCAGAACTATAAGAGTTTTGAAGATGGTTGAACCATGGCTAAAAAACAACCAGTTTTGCATTAAAGTTTTGAACCCTTACATGCCAACTGTGATTGAGCACCTAGAAAGACTACAAAGGAAACATGGAGGAATGCTTGTGAGAAATCCACTTTCACGAAACTCCACGCACGAAATGTACTGGATATCTAATGGCACAGGTAACATTGTCTCTTCAGTCAACATGGTGTCTAGATTGCTACTGAACAGGTTCACGATGACACACAGGAGACCCACCATAGAGAAAGATGTGGATTTAGGAGCAGGAACTCGACATGTTAATGCGGAACCAGAAACACCCAACATGGATGTCATTGGGGAAAGAATAAAAAGGATCAAGGAGGAGCATAATTCAACATGGCACTATGATGACGAAAACCCCTACAAAACGTGGGCTTACCATGGATCCTATGAAGTCAAAGCCACAGGCTCAGCCTCCTCCATGATAAATGGAGTCGTGAAACTCCTCACCAAACCATGGGATGTGGTGCCCATGGTGACACAGATGGCAATGACAGACACAACTCCATTTGGCCAGCAGAGAGTCTTTAAAGAGAAAGTGGACACCAGGACGCCCAGGCCCATGCCAGGGACAAGAAAGGCTATGGAGATCACAGCGGAGTGGCTCTGGAGAACCCTGGGAAGGAACAAAAGACCCAGATTATGCACAAGGGAAGAGTTTACAAAAAAGGTCAGAACTAACGCAGCCATGGGCGCCGTTTTCACAGAGGAGAACCAATGGGACAGTGCGAAAGCTGCTGTTGAGGATGAAGAATTTTGGAAACTTGTGGACAGAGAACGTGAACTCCACAAATTGGGCAAATGTGGAAGCTGCGTTTATAACATGATGGGCAAGAGAGAGAAAAAACTTGGAGAGTTTGGCAAAGCAAAAGGCAGTAGAGCTATATGGTACATGTGGTTGGGAGCCAGGTACCTTGAGTTCGAAGCCCTTGGATTCTTAAATGAAGACCACTGGTTCTCGCGTGAAAACTCTTACAGTGGAGTAGAAGGAGAAGGACTGCACAAGCTAGGCTACATATTAAGGGACATTTCCAAGATACCCGGAGGAGCCATGTATGCTGATGACACAGCTGGTTGGGACACAAGAATAACAGAAGATGACCTGCACAATGAGGAAAAGATCATACAGCAAATGGACCCTGAACACAGGCAGTTAGCGAACGCTATATTCAAGCTCACATACCAAAACAAAGTGGTCAAAGTTCAACGACCGACTCCAACGGGCACGGTAATGGATATTATATCTAGGAAAGACCAAAGGGGCAGTGGACAACTGGGAACTTATGGCCTGAATACATTCACCAACATGGAAGCCCAGTTAGTCAGACAAATGGAAGGAGAAGGTGTGCTGACAAAGGCAGACCTCGAGAACCCTCATCTGCTAGAGAAGAAAATCACACAATGGTTGGAAACCAAAGGAGTGGAGAGGTTAAAAAGAATGGCCATTAGCGGGGATGATTGCGTGGTGAAACCAATCGATGACAGGTTCGCTAATGCCCTGCTTGCTTTGAACGATATGGGAAAGGTTCGGAAAGACATACCTCAATGGCAGCCATCAAAGGGATGGCATGATTGGCAACAGGTTCCTTTCTGCTCCCACCACTTTCATGAATTGATCATGAAAGATGGAAGAAAGTTGGTGGTTCCCTGCAGACCCCAGGACGAACTAATAGGAAGAGCAAGAATCTCTCAAGGAGCGGGATGGAGCCTTAGAGAAACTGCATGTCTGGGGAAAGCCTACGCCCAAATGTGGAGTCTCATGTATTTTCACAGAAGAGATCTCAGATTAGCATCCAACGCCATATGTTCAGCAGTACCAGTCCACTGGGTTCCCACAAGTAGAACGACATGGTCTATTCATGCTCACCATCAGTGGATGACTACAGAAGACATGCTTACTGTTTGGAACAGGGTGTGGATAGAGGAAAATCCATGGATGGAAGACAAAACTCCAGTTACAACTTGGGAAAATGTTCCATATCTAGGAAAGAGAGAAGACCAATGGTGTGGATCACTTATTGGTCTCACTTCCAGAGCAACCTGGGCCCAGAACATACCCACAGCAATTCAACAGGTGAGAAGCCTTATAGGCAATGAAGAGTTCCTGGACTACATGCCTTCAATGAAGAGATTCAGGAAGGAAGAGGAGTCGGAGGGAGCCATTTGGTAAACGTAGGAAGTGGAAAAGAGGCTAACTGTCAGGCCACCTTAAGCCACAGTACGGAAGAAGCTGTGCTGCCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGAAGTCAGGCCCCAAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGTCGTGGGGACGTAAAACCTGGGAGGCTGCAAACTGTGGAAGCTGTACGCACGGTGTAGCAGACTAGCGGTTAGAGGAGACCCCTCCCATGACACAACGCAGCAGCGGGGCCCGAGCACTGAGGGAAGCTGTACCTCCTTGCAAAGGACTAGAGGTTAGAGGAGACCCCCCGCAAATAAAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT", "2K": "TPQDNQLAYVVIGILTLAATIAA", "C": "MNNQRKKTGKPSINMLKRVRNRVSTGSQLAKRFSKGLLNGQGPMKLVMAFIAFLRFLAIPPTAGVLARWGTFKKSGAIKVLKGFKKEISNMLSIINQRKKTSLCLMMILPAALA", "E": "MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWASGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQNSGGTSIFAGHLKCRLKMDKLELKGMSYAMCTNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDNALKINWYKKGSSIGKMFEATERGARRMAILGDTAWDFGSVGGVLNSLGKMVHQIFGSAYTALFSGVSWVMKIGIGVLLTWIGLNSKNTSMSFSCIAIGIITLYLGAVVQA", "M": "FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVTYKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVGMGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQKVVIFILLMLVTPSMT", "NS1": "DMGCVINWKGKELKCGSGIFVTNEVHTWTEQYKFQADSPKRLATAIAGAWENGVCGIRSTTRMENLLWKQIANELNYILWENNIKLTVVVGDTLGVLEQGKRTLTPQPMELKYSWKTWGKAKIVTAETQNSSFIIDGPNTPECPSASRAWNVWEVEDYGFGVFTTNIWLKLREVYTQLCDHRLMSAAVKDERAVHADMGYWIESQKNGSWKLEKASLIEVKTCTWPKSHTLWTNGVLESDMIIPKSLAGPISQHNYRPGYHTQTAGPWHLGKLELDFNYCEGTTVVITESCGTRGPSLRTTTVSGKLIHEWCCRSCTLPPLRYMGEDGCWYGMEIRPISEKEENMVKSLVSA", "NS2A": "GSGKVDNFTMGVLCLAILFEEVLRGKFGKKHMIAGVFFTFVLLLSGQITWRDMAHTLIMIGSNASDRMGMGVTYLALIATFKIQPFLALGFFLRKLTSRENLLLGVGLAMATTLQLPEDIEQMANGVALGLMALKLITQFETYQLWTALVSLTCSNTIFTLTVAWRTATLILAGVSLLPVCQSSSMRKTDWLPMTVAAMGVPPLPLFIFSLKDTLKRR", "NS2B": "SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSADLTVEKAPDVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLKTALLIVSGIFPYSIPATLLVWHTWQKQTQR", "NS3": "SGVLWDVPSPPETQKAELEEGVYRIKQQGIFGKTQVGVGVQKEGVFHTMWHVTRGAVLTHNGKRLEPNWASVKKDLISYGGGWRLSAQWQKGEEVQVIAVEPGKNPKNFQTTPGTFQTTTGEIGAIALDFKPGTSGSPIINREGKVVGLYGNGVVTKNGGYVSGIAQTNAEPDGPTPELEEEMFKKRNLTIMDLHPGSGKTRKYLPAIVREAIKRRLRTLILAPTRVVAAEMEEALKGLPIRYQTTATKSEHTGREIVDLMCHATFTMRLLSPVRVPNYNLIIMDEAHFTDPASIAARGYISTRVGMGEAAAIFMTATPPGTADAFPQSNAPIQDEERDIPERSWNSGNEWITDFAGKTVWFVPSIKAGNDIANCLRKNGKKVIQLSRKTFDTEYQKTKLNDWDFVVTTDISEMGANFKADRVIDPRRCLKPVILTDGPERVILAGPMPVTAASAAQRRGRVGRNPQKENDQYIFTGQPLNNDEDHAHWTEAKMLLDNINTPEGIIPALFEPEREKSAAIDGEYRLKGESRKTFVELMRRGDLPVWLAHKVASEGIKYTDRKWCFDGQRNNQILEENMDVEIWTKEGEKKKLRPRWLDARTYSDPLALKEFKDFAAGRK", "NS4A": "SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEDGGRAYRHAVEELPETMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEVPLQWIASAIVLEFFMMVLLIPEPEKQR", "NS4B": "NEMGLLETTKRDLGMSKEPGVVSPTSYLDVDLHPASAWTLYAVATTVITPMLRHTIENSTANVSLAAIANQAVVLMGLDKGWPISKMDLGVPLLALGCYSQVNPLTLTAAVLLLITHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGIMTIDLDSVIFDSKFEKQLGQVMLLVLCAVQLLLMRTSWALCEALTLATGPITTLWEGSPGKFWNTTIAVSMANIFRGSYLAGAGLAFSIMKSVGTGKR", "NS5": "GTGSQGETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVVPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVNAEPETPNMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPMPGTRKAMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAAMGAVFTEENQWDSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQRGSGQLGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYMPSMKRFRKEEESEGAIW", "pr": 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"AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGACTCGGAAGCTTGCTTAACGTAGTGCTGACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGAAAACCGTCTATCAATATGCTGAAACGCGTGAGAAACCGTGTGTCAACTGGATCACAGTTGGCGAAGAGATTCTCAAGAGGATTGCTGAACGGCCAAGGACCAATGAAATTGGTTATGGCGTTCATAGCTTTCCTCAGATTTCTAGCCATTCCACCGACAGCAGGAGTCTTGGCTAGATGGGGTACCTTCAAGAAGTCGGGGGCTATTAAGGTCCTAAAAGGCTTCAAGAAGGAGATCTCAAACATGCTGAGCATTATCAACAAACGGAAAAAGACATCGCTCTGTCTCATGATGATGTTACCAGCAACACTTGCTTTCCACTTGACTTCACGAGATGGAGAGCCGCGCATGATTGTGGGGAAGAATGAAAGAGGAAAATCCCTACTTTTTAAGACAGCCTCTGGAATCAACATGTGCACACTCATAGCCATGGATTTGGGAGAGATGTGTGATGACACGGTCACTTACAAATGCCCCCACATTACCGAAGTGGAGCCTGAAGACATTGACTGCTGGTGCAACCTTACATCGACATGGGTGACTTATGGAACGTGCAATCAAGCTGGAGAGCATAGACGCGATAAGAGATCAGTGGCGTTAGCTCCCCATGTCGGCATGGGACTGGACACACGCACCCAAACCTGGATGTCGGCTGAAGGAGCTTGGAGACAAGTCGAGAAGGTAGAGACATGGGCCCTTAGGCACCCAGGGTTCACCATACTAGCCCTATTTCTTGCCCATTACATAGGCACTTCCTTGACCCAGAAAGTGGTTATTTTTATACTACTAATGCTGGTCACCCCATCCATGACAATGAGATGTGTGGGAGTAGGAAACAGAGATTTTGTGGAAGGCCTATCGGGAGCTACGTGGGTTGACGTGGTGCTCGAGCACGGTGGGTGTGTGACTACCATGGCTAAGAACAAGCCCACGCTGGATATAGAGCTTCAGAAGACCGAGGCCACCCAACTGGCGACCCTAAGGAAGCTATGCATTGAGGGAAAAATTACCAACATAACAACCGACTCAAGGTGTCCCACCCAAGGGGAAGCGATTTTACCTGAGGAGCAGGACCAGAACTACGTGTGTAAGCATACATACGTGGACAGAGGCTGGGGAAACGGTTGTGGTTTGTTTGGCAAGGGAAGCTTGGTGACATGCGCGAAATTTCAATGTTTAGAATCAATAGAGGGAAAAGTGGTGCAACATGAGAACCTCAAATACACCGTCATCATCACAGTGCACACAGGAGACCAACACCAGGTGGGAAATGAAACGCAGGGAGTCACGGCTGAGATAACACCCCAGGCATCAACCGCTGAAGCCATCTTACCTGAATATGGAACCCTTGGGCTAGAATGCTCACCACGGACAGGTTTGGATTTCAATGAAATGATCTTATTGACAATGAAGAACAAAGCATGGATGGTACATAGACAATGGTTCTTTGACCTACCTCTACCATGGACATCAGGAGCTACAACAGAAACACCAACCTGGAACAGGAAAGAGCTTCTTGTGACATTCAAAAACGCACATGCAAAAAAACAAGAAGTAGTTGTCCTTGGATCGCAAGAGGGAGCAATGCATACAGCACTGACAGGAGCTACAGAGATCCAAACCTCAGGAGGCACAAGCATTTTTGCGGGGCACTTAAAATGTAGACTCAAGATGGACAAATTGGAACTCAAGGGGATGAGCTATGCAATGTGCTTGAATACCTTTGTGTTGAAGAAAGAAGTCTCCGAAACGCAGCATGGGACAATACTCATTAAGGTTGAGTACAAAGGGGAAGATGCACCCTGCAAGATTCCTTTCTCCACGGAGGATGGACAAGGGAAAGCTCACAATGGCAGACTGATCACAGCCAACCCAGTGGTGACCAAGAAGGAGGAGCCTGTCAATATTGAGGCTGAACCTCCTTTTGGGGAAAGTAATATAGTAATTGGAATTGGAGACAAAGCCTTGAAAATCAACTGGTACAAGAAGGGAAGCTCGATTGGGAAGATGTTCGAGGCCACTGCCAGAGGTGCAAGGCGCATGGCCATCTTGGGAGACACAGCCTGGGACTTTGGATCAGTGGGTGGTGTTTTGAATTCATTAGGGAAAATGGTGCACCAAATATTTGGAAGTGCTTACACAGCCCTATTTAGTGGAGTCTCCTGGATAATGAAAATTGGAATAGGTGTCCTCTTAACCTGGATAGGGTTGAATTCAAAAAACACTTCTATGTCATTTTCATGCATTGCGATAGGAATCATTACACTCTATCTGGGAGCCGTGGTGCAAGCTGACATGGGGTGTGTCATAAACTGGAAAGGCAAAGAACTCAAATGTGGAAGTGGAATTTTCGTCACTAATGAGGTCCACACCTGGACAGAGCAATACAAATTTCAAGCAGACTCCCCCAAAAGACTGGCGACAGCCATTGCAGGCGCTTGGGAGAATGGAGTGTGCGGAATCAGGTCAACAACCAGAATGGAGAACCTCTTGTGGAAGCAAATAGCCAATGAACTGAACTACATATTATGGGAAAACAACATCAAATTAACGGTAGTTGTGGGCGACATAATTGGGGTCTTAGAGCAAGGGAAAAGAACACTAACACCACAACCCATGGAGCTAAAATATTCATGGAAAACATGGGGAAAGGCAAAAATAGTGACAGCTGAAACACAAAATTCCTCTTTCATAATAGATGGGCCAAACACACCGGAGTGTCCAAGTGCCTCAAGAGCATGGAATGTGTGGGAGGTGGAAGATTACGGGTTCGGAGTCTTCACAACCAACATATGGCTGAAACTCCGAGAGGTGTACACCCAACTATGTGACCATAGGCTAATGTCGGCAGCCGTCAAGGATGAGAGGGCCGTACACGCCGACATGGGCTATTGGATAGAAAGCCAAAAGAATGGAAGTTGGAAGCTAGAAAAAGCATCCCTCATAGAGGTGAAAACCTGCACATGGCCAAAATCACACACTCTTTGGAGCAATGGTGTGCTAGAGAGTGACATGATCATCCCAAAGAGTCTAGCTGGTCCTATTTCGCAACACAACCACAGGCCCGGGTACCACACCCAAACGGCAGGACCCTGGCACTTAGGAAAATTGGAGCTGGACTTCAACTATTGTGAAGGAACAACAGTTGTCATCACAGAAAACTGTGGGACAAGAGGCCCATCATTGAGAACAACAACAGTGTCAGGGAAGTTGATACACGAATGGTGTTGCCGCTCGTGCACACTTCCTCCCCTGCGATACATGGGAGAAGACGGCTGCTGGTATGGCATGGAAATTAGACCCATTAATGAGAAAGAAGAGAACATGGTAAAGTCTTTAGCCTCAGCAGGGAGTGGAAAGGTGGACAACTTCACAATGGGTGTCTTGTGTTTGGCAATCCTCTTTGAAGAGGTGATGAGAGGAAAATTTGGGAAAAAACACATGATTGCAGGGGTTCTCTTCACGTTTGTGCTCCTTCTCTCAGGGCAAATAACATGGAGAGACATGGCGCACACACTCATAATGATTGGGTCCAACGCCTCTGACAGAATGGGAATGGGCGTCACTTACCTAGCTTTAATTGCAACATTTAAAATTCAGCCATTCTTGGCTTTGGGATTCTTCCTGAGGAAACTGACATCTAGAGAAAATTTATTGTTGGGAGTTGGGTTGGCCATGGCAACAACGTTACAACTGCCAGAGGACATTGAACAAATGGCGAATGGAATTGCTTTGGGGCTCATGGCTCTTAAACTGATAACACAATTTGAAACATACCAACTATGGACGGCATTAGTCTCCCTAACGTGTTCAAATACAATTTTCACGTTGACTGTTGCCTGGAGAACAGCCACCCTGATTTTGGCCGGAATTTCGCTTTTGCCAGTGTGCCAGTCTTCGAGCATGAGGAAAACAGATTGGCTCCCAATGACTGTGGCAGCTATGGGAGTTCCACCCCTACCACTTTTTATCTTCAGTTTGAAAGATACACTCAAAAGGAGAAGCTGGCCACTGAATGAGGGGGTGATGGCTGTTGGACTTGTGAGCATTCTAGCTAGTTCTCTCCTTAGGAATGATGTGCCCATGGCTGGACCATTAGTGGCTGGGGGCTTGCTGATAGCGTGCTACGTCATAACTGGCACGTCAGCAGACCTCACTGTAGAAAAAGCAGCAGATGTAACATGGGAGGAAGAGGCTGAGCAAACAGGAGTGTCCCACAATTTAATGATCACAGTTGATGATGATGGAACAATGAGAATAAAAGATGATGAGACTGAGAACATCCTAACAGTGCTTTTAAAAACAGCATTACTAATAGTATCAGGCATCTTTCCATACTCCATACCCGCAACACTGTTGGTCTGGCATACTTGGCAAAAGCAAACCCAAAGATCCGGCGTCCTATGGGACGTACCCAGCCCCCCAGAGACACAGAAAGCAGAACTGGAAGAAGGGGTCTATAGGATCAAACAGCAAGGAATTTTTGGGAAAACCCAAGTGGGGGTTGGAGTACAGAAAGAAGGAGTTTTCCACACCATGTGGCACGTCACAAGAGGGGCAGTGTTGACACACAATGGGAAAAGACTGGAACCAAACTGGGCTAGCGTGAAAAAAGATCTGATTTCATACGGAGGAGGATGGAGATTGAGTGCACAATGGCAAAAGGGAGAGGAGGTGCAGGTTATTGCCGTAGAGCCTGGGAAGAACCCAAAGAACTTTCAAACCATGCCAGGCATTTTTCAGACAACAACAGGGGAAATAGGAGCAATTGCACTGGACTTCAAGCCTGGAACTTCAGGATCTCCCATCATAAACAGAGAGGGAAAGGTAGTGGGACTGTATGGCAATGGAGTGGTTACAAAGAATGGTGGCTATGTCAGTGGAATAGCGCAAACAAATGCAGAACCAGACGGACCGACACCAGAGTTGGAAGAAGAGATGTTCAAAAAGCGAAATCTAACCATAATGGATCTTCATCCTGGGTCAGGAAAGACGCGGAAATACCTTCCAGCTATTGTTAGAGAGGCAATCAAGAGACGCTTAAGGACTCTAATTTTGGCACCAACAAGGGTGGTTGCAGCTGAGATGGAAGAAGCATTGAAAGGGCTCCCAATAAGGTATCAAACAACTGCAACAAAATCTGAACACACAGGAAGAGAGATTGTTGATCTAATGTGCCACGCAACGTTCACAATGCGCTTGCTGTCACCAGTCAGGGTTCCAAACTACAACTTGATAATAATGGATGAGGCTCATTTCACAGACCCAGCCAGTATAGCGGCTAGAGGGTACATATCAACTCGTGTAGGAATGGGAGAGGCAGCCGCAATTTTCATGACAGCAACACCCCCTGGAACAGCTGATGCCTTTCCTCAGAGCAACGCTCCAATTCAAGATGAAGAAAGGGACATACCGGAACGCTCATGGAATTCAGGCAATGAATGGATTACCGACTTTGTTGGGAAGACGGTGTGGTTTGTCCCTAGCATCAAAGCCGGAAATGACATAGCAAACTGCTTGCGGAAAAACGGAAAAAAGGTCATTCAACTTAGTAGGAAGACTTTTGACACAGAATATCAAAAGACTAAACTGAATGATTGGGACTTTGTGGTGACAACAGACATTTCAGAAATGGGAGCCAATTTCAAAGCAGATAGAGTGATCGACCCAAGAAGATGTCTCAAGCCAGTGATTTTGACAGATGGACCCGAGCGGGTGATCCTGGCTGGACCAATGCCAGTCACCGTAGCGAGCGCTGCGCAAAGGAGAGGGAGAGTTGGCAGGAACCCACAAAAAGAAAATGACCAGTACATATTCACGGGCCAGCCTCTCAACAATGATGAAGACCATGCTCACTGGACAGAAGCAAAAATGCTGCTGGACAACATCAACACACCAGAAGGGATTATACCAGCTCTCTTTGAACCAGAAAGGGAGAAGTCAGCCGCCATAGACGGCGAATACCGCCTGAAGGGTGAGTCCAGGAAGACCTTCGTGGAACTCATGAGGAGGGGTGACCTCCCAGTTTGGCTAGCCCATAAAGTAGCATCAGAAGGGATCAAATATACAGATAGAAAATGGTGCTTTGATGGAGAACGTAATAATCAAATTTTAGAGGAGAATATGGATGTGGAAATCTGGACAAAGGAAGGAGAAAAGAAAAAATTGAGACCTAGGTGGCTTGATGCCCGCACTTATTCAGATCCCTTAGCACTCAAGGAATTCAAGGATTTTGCAGCTGGCAGAAAGTCAATCGCCCTTGATCTTGTGACAGAAATAGGAAGAGTGCCTTCACACTTAGCCCACAGAACGAGAAACGCCCTGGACAATTTGGTGATGCTGCACACGTCAGAACATGGCGGTAGGGCCTACAGGCATGCAGTGGAGGAACTACCAGAAACAATGGAAACACTCTTACTCCTGGGACTCATGATCTTGTTAACAGGTGGAGCAATGCTTTTCTTGATATCAGGTAAAGGGATTGGAAAGACTTCAATAGGACTCATTTGTGTAATTGCTTCCAGCGGCATGTTATGGATGGCTGATGTCCCACTCCAATGGATCGCGTCGGCTATAGTCCTGGAGTTTTTTATGATGGTGTTGCTCATACCAGAACCAGAAAAGCAGAGAACTCCCCAAGACAACCAACTCGCATATGTCGTGATAGGCATACTTACATTGGCTGCAATAGTAGCAGCCAATGAAATGGGACTGTTGGAAACTACAAAGAGAGATTTAGGAATGTCTAAAGAACCAGGTGTTGTTTCTCCAACCAGCTATTTGGATGTGGACTTGCACCCAGCATCAGCCTGGACATTGTACGCCGTGGCCACAACAGTAATAACACCAATGTTGAGACATACCATAGAGAATTCCACAGCAAATGTGTCCCTGGCAGCTATAGCTAACCAGGCAGTGGTCCTGATGGGTTTAGACAAAGGATGGCCGATATCGAAAATGGACTTAGGCGTACCACTACTGGCACTGGGTTGCTATTCACAAGTGAACCCACTAACTCTCACAGCGGCAGTACTTTTGCTAGTCACACATTATGCTATTATAGGTCCAGGATTGCAGGCAAAAGCCACTCGTGAAGCTCAGAAAAGGACAGCTGCTGGAATAATGAAGAATCCAACGGTGGATGGGATAATGACAATAGACCTAGATCCTGTAATATACGATTCAAAATTTGAAAAGCAACTAGGACAGGTTATGCTCCTGGTTCTGTGTGCAGTTCAACTTTTGTTAATGAGAACATCATGGGCCTTGTGTGAAGCTCTAACCCTAGCCACAGGACCAATAACAACACTCTGGGAAGGATCACCTGGGAAGTTTTGGAACACCACGATAGCTGTTTCCATGGCGAACATCTTTAGAGGGAGCTATTTAGCAGGAGCTGGGCTTGCTTTTTCTATCATGAAATCAGTTGGAACAGGAAAGAGAGGAACAGGGTCACAAGGTGAAACCTTAGGAGAAAAGTGGAAAAAGAAATTAAATCAGTTATCCCGGAAAGAGTTTGACCTTTACAAGAAATCCGGAATCACTGAAGTGGATAGAACAGAAGCCAAAGAAGGGTTGAAAAGAGGAGAAATAACACACCATGCCGTGTCCAGAGGCAGCGCAAAACTTCAATGGTTCGTGGAGAGAAACATGGTCATTCCCGAAGGAAGAGTCATAGACTTAGGCTGTGGAAGAGGAGGCTGGTCATATTACTGTGCAGGACTGAAAAAAGTTACAGAAGTGCGAGGATACACAAAAGGCGGCCCAGGACACGAAGAACCAGTACCTATGTCTACATACGGATGGAACATAGTCAAGTTAATGAGTGGAAAGGATGTGTTTTATCTTCCACCTGAAAAGTGTGATACCCTATTGTGTGACATTGGAGAATCTTCACCAAGCCCAACAGTGGAAGAAAGCAGAACCATAAGAGTCTTGAAGATGGTTGAACCATGGCTAAAAAACAACCAGTTTTGCATTAAAGTATTGAACCCTTACATGCCAACTGTGATTGAGCACCTAGAAAGACTACAAAGGAAACATGGAGGAATGCTTGTGAGAAATCCACTCTCACGAAACTCCACGCACGAAATGTACTGGATATCCAATGGTACAGGCAACATCGTCTCTTCAGTCAACATGGTATCCAGATTGCTACTGAACAGATTCACAATGACACACAGGAGACCCACCATAGAGAAAGATGTGGATTTAGGAGCAGGAACCCGACATGTCAATGCGGAACCAGAAACACCCAACATGGATGTCATTGGGGAAAGAATAAAAAGGATCAAGGAGGAGCATAGTTCAACATGGCACTATGATGATGAAAATCCTTACAAAACGTGGGCTTACCATGGATCCTATGAAGTCAAAGCCACAGGCTCAGCCTCCTCCATGATAAATGGAGTCGTGAAACTCCTCACAAAACCATGGGATGTGGTGCCCATGGTGACACAGATGGCAATGACAGATACAACCCCATTTGGCCAGCAAAGAGTTTTTAAAGAGAAAGTGGACACCAGGACACCCAGGCCCATGCCAGGAACAAGAAAGGTTATGGAGATCACAGCGGAGTGGCTTTGGAGAACCCTGGGAAGGAACAAAAGACCCAGATTATGCACAAGGGAGGAGTTCACAAAAAAGGTCAGAACCAACGCAGCTATGGGCGCCGTTTTCACAGAGGAGAACCAATGGGACAGTGCGAGAGCTGCTGTTGAGGACGAAGAATTTTGGAAACTTGTGGACAGAGAACGTGAACTCCACAAATTGGGCAAGTGTGGAAGCTGCGTTTACAACATGATGGGCAAGAGAGAGAAGAAACTTGGAGAGTTTGGCAAAGCAAAAGGCAGTAGAGCTATATGGTACATGTGGTTGGGAGCCAGGTACCTTGAGTTCGAGGCACTCGGATTCTTAAATGAAGACCACTGGTTCTCGCGTGAAAACTCTTACAGTGGAGTAGAAGGAGAAGGACTGCACAAGCTGGGATACATCTTAAGAGATATTTCCAAGATACCCGGAGGAGCTATGTATGCTGATGACACAGCTGGTTGGGACACAAGAATAACAGAAGATGACCTGCACAATGAGGAAAAAATCACACAGCAAATGGACCCTGAACACAGGCAGTTAGCGAACGCTATATTCAAGCTCACATACCAAAACAAAGTGGTCAAAGTTCAACGACCAACTCCAAAGGGCACGGTAATGGACATCATATCTAGGAAAGACCAAAGAGGCAGTGGACAGGTGGGAACTTATGGTCTGAATACATTCACCAACATGGAAGCCCAGTTAATCAGACAAATGGAAGGAGAAGGTGTGTTGTCAAAGGCAGACCTCGAGAACCCTCATCTGCTAGAGAAGAAAATTACACAATGGTTGGAAACCAAAGGAGTGGAGAGGTTAAAAAGAATGGCCATCAGCGGGGATGATTGCGTAGTGAAACCAATCGATGACAGGTTCGCCAATGCCCTGCTTGCCCTGAACGATATGGGAAAGGTTAGGAAGGACATACCTCAATGGCAGCCATCAAAGGGATGGCATGATTGGCAACAGGTCCCTTTCTGCTCCCACCACTTTCATGAATTGATCATGAAAGATGGAAGAAAGTTGGTAGTTCCCTGCAGACCCCAGGACGAACTAATAGGAAGAGCGAGAATCTCTCAAGGAGCAGGATGGAGCCTTAGAGAAACTGCATGTCTAGGGAAAGCCTACGCTCAAATGTGGACTCTCATGTATTTTCACAGAAGAGATCTTAGACTAGCATCCAACGCCATATGTTCAGCAGTACCAGTCCATTGGGTCCCCACAAGCAGAACGACATGGTCTATTCATGCTCACCATCAGTGGATGACTACAGAAGACATGCTTACTGTCTGGAACAGGGTGTGGATAGAGGACAATCCATGGATGGAAGACAAAACTCCAGTCACAACTTGGGAAGATGTTCCATATCTAGGGAAGAGAGAAGACCAATGGTGCGGATCACTCATTGGTCTCACTTCCAGAGCAACCTGGGCCCAGAACATACTCACAGCAATCCAACAGGTGAGAAGCCTTATAGGCAATGAAGAGTTTCTGGACTACATGCCTTCGATGAAGAGATTCAGGAAGGAGGAGGAGTCAGAGGGAGCCATTTGGTAAACGCAGGAAGTGAAAAAGAGGCAAACTGTCAGGCCACCTTAAGCCACAGTACGGAAGAAGCTGTGCAGCCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGAAGTCAGGCCCAAAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGTCGTGGGGACGTAAAGCCTGGGAGGCTGCAAACCGTGGAAGCTGTACGCACGGTGTAGCAGACTAGCGGTTAGAGGAGACCCCTCCCATGACACAACGCAGCAGCGGGGCCCGAGCACTGAGGGAAGCTGTACCTCCTTGCAAAGGACTAGAGGTTAGAGGAGACCCCCCGCAAATAAAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT", "2K": "TPQDNQLAYVVIGILTLAAIVAA", "C": "MNNQRKKTGKPSINMLKRVRNRVSTGSQLAKRFSRGLLNGQGPMKLVMAFIAFLRFLAIPPTAGVLARWGTFKKSGAIKVLKGFKKEISNMLSIINKRKKTSLCLMMMLPATLA", "E": "MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAILPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLESIEGKVVQHENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTAEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWTSGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQTSGGTSIFAGHLKCRLKMDKLELKGMSYAMCLNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDKALKINWYKKGSSIGKMFEATARGARRMAILGDTAWDFGSVGGVLNSLGKMVHQIFGSAYTALFSGVSWIMKIGIGVLLTWIGLNSKNTSMSFSCIAIGIITLYLGAVVQADM", "M": "FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVTYKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVGMGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQKVVIFILLMLVTPSMT", "NS1": "DMGCVINWKGKELKCGSGIFVTNEVHTWTEQYKFQADSPKRLATAIAGAWENGVCGIRSTTRMENLLWKQIANELNYILWENNIKLTVVVGDIIGVLEQGKRTLTPQPMELKYSWKTWGKAKIVTAETQNSSFIIDGPNTPECPSASRAWNVWEVEDYGFGVFTTNIWLKLREVYTQLCDHRLMSAAVKDERAVHADMGYWIESQKNGSWKLEKASLIEVKTCTWPKSHTLWSNGVLESDMIIPKSLAGPISQHNHRPGYHTQTAGPWHLGKLELDFNYCEGTTVVITENCGTRGPSLRTTTVSGKLIHEWCCRSCTLPPLRYMGEDGCWYGMEIRPINEKEENMVKSLASA", "NS2A": "GSGKVDNFTMGVLCLAILFEEVMRGKFGKKHMIAGVLFTFVLLLSGQITWRDMAHTLIMIGSNASDRMGMGVTYLALIATFKIQPFLALGFFLRKLTSRENLLLGVGLAMATTLQLPEDIEQMANGIALGLMALKLITQFETYQLWTALVSLTCSNTIFTLTVAWRTATLILAGISLLPVCQSSSMRKTDWLPMTVAAMGVPPLPLFIFSLKDTLKRR", "NS2B": "SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSADLTVEKAADVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLKTALLIVSGIFPYSIPATLLVWHTWQKQTQR", "NS3": "SGVLWDVPSPPETQKAELEEGVYRIKQQGIFGKTQVGVGVQKEGVFHTMWHVTRGAVLTHNGKRLEPNWASVKKDLISYGGGWRLSAQWQKGEEVQVIAVEPGKNPKNFQTMPGIFQTTTGEIGAIALDFKPGTSGSPIINREGKVVGLYGNGVVTKNGGYVSGIAQTNAEPDGPTPELEEEMFKKRNLTIMDLHPGSGKTRKYLPAIVREAIKRRLRTLILAPTRVVAAEMEEALKGLPIRYQTTATKSEHTGREIVDLMCHATFTMRLLSPVRVPNYNLIIMDEAHFTDPASIAARGYISTRVGMGEAAAIFMTATPPGTADAFPQSNAPIQDEERDIPERSWNSGNEWITDFVGKTVWFVPSIKAGNDIANCLRKNGKKVIQLSRKTFDTEYQKTKLNDWDFVVTTDISEMGANFKADRVIDPRRCLKPVILTDGPERVILAGPMPVTVASAAQRRGRVGRNPQKENDQYIFTGQPLNNDEDHAHWTEAKMLLDNINTPEGIIPALFEPEREKSAAIDGEYRLKGESRKTFVELMRRGDLPVWLAHKVASEGIKYTDRKWCFDGERNNQILEENMDVEIWTKEGEKKKLRPRWLDARTYSDPLALKEFKDFAAGRK", "NS4A": "SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPETMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMADVPLQWIASAIVLEFFMMVLLIPEPEKQR", "NS4B": "NEMGLLETTKRDLGMSKEPGVVSPTSYLDVDLHPASAWTLYAVATTVITPMLRHTIENSTANVSLAAIANQAVVLMGLDKGWPISKMDLGVPLLALGCYSQVNPLTLTAAVLLLVTHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGIMTIDLDPVIYDSKFEKQLGQVMLLVLCAVQLLLMRTSWALCEALTLATGPITTLWEGSPGKFWNTTIAVSMANIFRGSYLAGAGLAFSIMKSVGTGKR", "NS5": "GTGSQGETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGEITHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVNAEPETPNMDVIGERIKRIKEEHSSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPMPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAAMGAVFTEENQWDSARAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKITQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPKGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGVLSKADLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLRETACLGKAYAQMWTLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEDNPWMEDKTPVTTWEDVPYLGKREDQWCGSLIGLTSRATWAQNILTAIQQVRSLIGNEEFLDYMPSMKRFRKEEESEGAIW", "pr": "FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVTYKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKR"}} \ No newline at end of file diff --git a/nextclade/datasets/denv4/genome_annotation.gff3 b/nextclade/datasets/denv4/genome_annotation.gff3 index a417d706..0b573bda 100644 --- a/nextclade/datasets/denv4/genome_annotation.gff3 +++ b/nextclade/datasets/denv4/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_002640.1 1 10649 -NC_002640.1 feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; -NC_002640.1 feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; -NC_002640.1 feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; -NC_002640.1 feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; -NC_002640.1 feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_002640.1 feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_002640.1 feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_002640.1 feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_002640.1 feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_002640.1 feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; -NC_002640.1 feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_002640.1 feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome 1 10649 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/datasets/denv4/pathogen.json b/nextclade/datasets/denv4/pathogen.json index ee6e6797..d5ce36c8 100644 --- a/nextclade/datasets/denv4/pathogen.json +++ b/nextclade/datasets/denv4/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/datasets/denv4/reference.fasta b/nextclade/datasets/denv4/reference.fasta index 1abd4ccc..a6b134fc 100644 --- a/nextclade/datasets/denv4/reference.fasta +++ b/nextclade/datasets/denv4/reference.fasta @@ -1,179 +1,2 @@ ->NC_002640.1 Dengue virus 4, complete genome -AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAG -TTCTAACAGTTTGTTTGAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGG -TGGTTAGACCACCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAG -GGTTGGTGAAGAGATTCTCAACCGGACTTTTTTCTGGGAAAGGACCCTTACGGATGGTGC -TAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAGA -GATGGGGACAGTTGAAGAAAAATAAGGCCATCAAGATACTGATTGGATTCAGGAAGGAGA -TAGGCCGCATGCTGAACATCTTGAACGGGAGAAAAAGGTCAACGATAACATTGCTGTGCT -TGATTCCCACCGTAATGGCGTTTTCCCTCAGCACAAGAGATGGCGAACCCCTCATGATAG -TGGCAAAACATGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAAT -GCACTCTCATTGCCATGGACTTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCC -CCCTACTGGTCAATACCGAACCTGAAGACATTGATTGCTGGTGCAACCTCACGTCTACCT -GGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAG -CTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGGATGTCATCGG -AAGGGGCTTGGAAGCATGCTCAGAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCG -CGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCT -TCTTTGTCCTAATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAA -ACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATG -GAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGA -CAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACA -TAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACC -AACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGT -TTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCA -ATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACA -CCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGT -CACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCA -GGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCG -TGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAG -AGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGAC -AGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCA -CAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTTAAGTGCAAAGTCC -GTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAA -TTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAG -GTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGG -TTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAG -AATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAA -CACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAG -GTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGAC -TGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGT -TTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCA -CGAACTCGAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGT -TTCTGGGCTTCACAGTTCAAGCAGACATGGGTTGTGTGGCGTCATGGAGTGGGAAAGAAT -TGAAGTGTGGAAGCGGAATTTTTGTGGTTGACAACGTGCACACTTGGACAGAACAGTACA -AATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCTGCAATATTAAATGCCCACAAAGATG -GGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAGCAAATAACCA -ACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTAGTGGCTGGGGATG -TGAAGGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCCCCAGTGAGTGATCTGAAAT -ATTCATGGAAGACATGGGGAAAAGCAAAAATCTTCACCCCAGAAGCAAGAAATAGCACAT -TTTTAATAGACGGACCAGACACCTCTGAATGCCCCAATGAACGAAGAGCATGGAACTCTC -TTGAGGTGGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTCCGAG -AAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCTGCAATTAAAGATCAGAAAG -CTGTGCATGCTGACATGGGTTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAG -AGAAAGCATCTCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACCCACACACTGTGGA -GCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAATCATATGCGGGCCCTTTTTCAC -AGCACAATTACCGCCAGGGCTATGCCACGCAAACCGTGGGCCCATGGCACTTAGGCAAAT -TAGAGATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACC -ATAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAACTAGTCACGCAATGGTGCT -GCCGCTCCTGCACGATGCCTCCCTTAAGGTTCTTGGGAGAAGATGGGTGCTGGTATGGGA -TGGAGATTAGGCCCTTGAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGACGGCCG -GACAGGGCACATCAGAAACTTTTTCTATGGGTCTGTTGTGCCTGACCTTGTTTGTGGAAG -AATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTAGTTGTGGTGATCACTCTTT -GTGCTATCATCCTGGGAGGCCTCACATGGATGGACTTACTACGAGCCCTCATCATGTTGG -GGGACACTATGTCTGGTAGAATAGGAGGACAGATCCACCTAGCCATCATGGCAGTGTTCA -AGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAG -CACTAATGGTAATAGGAATGGCCATGACAACGGTGCTTTCAATTCCACATGACCTTATGG -AACTCATTGATGGAATATCACTGGGACTAATTTTGCTAAAAATAGTAACACAGTTTGACA -ACACCCAAGTGGGAACCTTAGCTCTTTCCTTGACTTTCATAAGATCAACAATGCCATTGG -TCATGGCTTGGAGGACCATTATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTGTGCA -GGACAAGCTGTCTTCAAAAACAGTCTCATTGGGTAGAAATAACAGCACTCATCCTAGGAG -CCCAAGCTCTGCCAGTGTACCTAATGACTCTTATGAAAGGAGCCTCAAGAAGATCTTGGC -CTCTTAACGAGGGCATAATGGCTGTGGGTTTGGTTAGTCTCTTAGGAAGCGCTCTTTTAA -AGAATGATGTCCCTTTAGCTGGCCCAATGGTGGCAGGAGGCTTACTTCTGGCGGCTTACG -TGATGAGTGGTAGCTCAGCAGATCTGTCACTAGAGAAGGCCGCCAACGTGCAGTGGGATG -AAATGGCAGACATAACAGGCTCAAGCCCAATCGTAGAAGTGAAGCAGGATGAAGATGGCT -CTTTCTCCATACGGGACGTCGAGGAAACCAATATGATAACCCTTTTGGTGAAACTGGCAC -TGATAACAGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACCTTATGGTACA -TGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTCCCCTCACCCGCTGCCA -CTAAAAAAGCCGCACTGTCTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTATTCGGGA -AAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAA -CAAGAGGATCAGTGATCTGCCACGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCA -GGAATGACATGATATCATACGGTGGGGGATGGAGGCTTGGAGACAAATGGGACAAAGAAG -AAGACGTTCAGGTCCTCGCCATAGAACCAGGAAAAAATCCTAAACATGTCCAAACGAAAC -CTGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTAGATTTCAAACCCG -GAACGTCTGGTTCTCCCATCATCAACAGGAAAGGAAAAGTCATCGGACTCTATGGAAATG -GAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGAG -AGCCAGATTATGAAGTGGATGAGGACATTTTTCGAAAGAAAAGATTAACTATAATGGACT -TACACCCCGGAGCTGGAAAGACAAAAAGAATTCTTCCATCAATAGTGAGAGAAGCCTTAA -AAAGGAGGCTACGAACTTTGATTTTAGCTCCCACGAGAGTGGTGGCGGCCGAGATGGAAG -AGGCCCTACGTGGACTGCCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAG -GAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTTTTGTCATCAA -CCAGGGTTCCAAATTACAACCTTATAGTGATGGATGAAGCACATTTCACCGATCCTTCTA -GTGTCGCGGCTAGAGGATACATCTCGACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCT -TCATGACCGCAACCCCTCCCGGAGCGACAGATCCCTTTCCCCAGAGCAACAGCCCAATAG -AAGACATCGAGAGGGAAATTCCGGAAAGGTCATGGAACACAGGGTTCGACTGGATAACAG -ACTACCAAGGGAAAACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAA -ATTGTTTGAGAAAGTCGGGAAAGAAAGTTATCCAGTTGAGTAGGAAAACCTTTGATACAG -AGTATCCAAAAACGAAACTCACGGACTGGGACTTTGTGGTCACTACAGACATATCTGAAA -TGGGGGCCAATTTTAGAGCCGGGAGAGTGATAGACCCTAGAAGATGCCTCAAGCCAGTTA -TCCTACCAGATGGGCCAGAGAGAGTCATTTTAGCAGGTCCTATTCCAGTGACTCCAGCAA -GCGCTGCTCAGAGAAGAGGGCGAATAGGAAGGAACCCAGCACAAGAAGACGACCAATACG -TTTTCTCCGGAGACCCACTAAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGA -TGCTGCTTGACAATATCTACACCCCAGAAGGGATCATTCCAACATTGTTTGGTCCGGAAA -GGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTT -TTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCTG -CTGGCATTTCTTACGAAGATCGGGAATGGTGCTTCACAGGGGAAAGAAATAACCAAATTT -TAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAGCTAAGGC -CAAGATGGTTAGATGCACGTGTATACGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGT -TTGCCAGTGGAAGGAAGAGTATAACTCTCGACATCCTAACAGAGATTGCCAGTTTGCCAA -CTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGATAACATAGTCATGCTCCACACAACAG -AAAGAGGAGGGAGGGCCTATCAACACGCCCTGAACGAACTTCCGGAGTCACTGGAAACAC -TCATGCTTGTAGCTTTACTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTCATGCAAG -GGAAAGGAATAGGGAAATTGTCAATGGGTTTGATAACCATTGCGGTGGCTAGTGGCTTGC -TCTGGGTAGCAGAAATTCAACCCCAGTGGATAGCGGCCTCAATCATACTAGAGTTTTTTC -TCATGGTACTGTTGATACCGGAACCAGAAAAACAAAGGACCCCACAAGACAATCAATTGA -TCTACGTCATATTGACCATTCTCACCATCATTGGTCTAATAGCAGCCAACGAGATGGGGC -TGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCC -TCGATGTGGACTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACAATTC -TGACTCCCATGCTGAGACACACCATAGAAAACACGTCGGCCAACCTATCTCTAGCAGCCA -TTGCCAACCAGGCAGCCGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGG -ACCTCGGTGTGCCGCTGTTAGCAATGGGATGCTATTCTCAAGTGAACCCAACAACCTTGA -CAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGCCCAGGATTGCAGGCAA -AAGCCACAAGAGAGGCCCAGAAAAGGACAGCTGCTGGGATCATGAAAAATCCCACAGTGG -ACGGGATAACAGTAATAGATCTAGAACCAATATCCTATGACCCAAAATTTGAAAAGCAAT -TAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACAT -GGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAATCTTGACCTTGTGGGAGGGCA -ACCCGGGAAGGTTTTGGAACACGACCATAGCCGTATCCACCGCCAACATTTTCAGGGGAA -GTTACTTGGCGGGAGCTGGACTGGCTTTTTCACTCATAAAGAATGCACAAACCCCTAGGA -GGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCAT -TAGACAGAAAAGAGTTTGAAGAGTATAAAAGAAGTGGAATACTAGAAGTGGACAGGACTG -AAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTATCAAGAGGGTCCA -GTAAGATCAGATGGATTGTTGAGAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTAGATC -TTGGCTGTGGGAGAGGAGGATGGTCTTATTACATGGCGACACTCAAGAACGTGACTGAAG -TGAAAGGGTATACAAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACTTATG -GTTGGAATTTGGTCAAACTCCATTCAGGGGTTGACGTGTTCTACAAACCCACAGAGCAAG -TGGACACCCTGCTCTGTGATATTGGGGAGTCATCTTCTAATCCAACAATAGAGGAAGGAA -GAACATTAAGAGTTTTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCA -TCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAGCTGGAGAAACTGCAGAGAA -AACATGGTGGGAACCTTGTCAGATGCCCGCTGTCCAGGAACTCCACCCATGAGATGTATT -GGGTGTCAGGAGCGTCGGGAAACATTGTGAGCTCTGTGAACACAACATCAAAGATGTTGT -TGAACAGGTTCACAACAAGGCATAGGAAACCCACTTATGAGAAGGACGTAGATCTTGGGG -CAGGAACGAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAA -GGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACCTGGCATTATGATCAGGAAAACCCAT -ACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCTGCATCCTCCA -TGGTGAACGGGGTGGTAAAACTGCTAACAAAACCCTGGGATGTGATTCCAATGGTGACTC -AGTTAGCCATGACAGATACAACCCCTTTTGGGCAACAAAGAGTGTTCAAAGAGAAGGTGG -ATACCAGAACACCACAACCAAAACCCGGTACACGAATGGTTATGACCACGACAGCCAATT -GGCTGTGGGCCCTCCTTGGAAAGAAGAAAAATCCCAGACTGTGCACAAGGGAAGAGTTCA -TCTCAAAAGTTAGATCAAACGCAGCCATAGGCGCAGTCTTTCAGGAAGAACAGGGATGGA -CATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGG -CCCTACACCAGGAAGGGAAATGTGAATCGTGTGTCTATAACATGATGGGAAAACGTGAGA -AAAAGTTAGGAGAGTTTGGCAGAGCCAAGGGAAGCCGAGCAATCTGGTACATGTGGCTGG -GAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTTTTGAATGAAGATCACTGGTTTGGCA -GAGAAAATTCATGGAGTGGAGTGGAAGGGGAAGGTCTGCACAGATTGGGATATATCCTGG -AGGAGATAGACAAGAAGGATGGAGACCTAATGTATGCTGATGACACAGCAGGCTGGGACA -CAAGAATCACTGAGGATGACCTTCAAAATGAGGAACTGATCACGGAACAGATGGCTCCCC -ACCACAAGATCCTAGCCAAAGCCATTTTCAAACTAACCTATCAAAACAAAGTGGTGAAAG -TCCTCAGACCCACACCGCGGGGAGCGGTGATGGATATCATATCCAGGAAAGACCAAAGAG -GTAGTGGACAAGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTTCAACTCA -TCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGT -TGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTAAAGAGGATGG -CAATCAGTGGAGACGATTGCGTGGTGAAGCCCCTAGATGAGAGGTTTGGCACTTCCCTCC -TCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCTAAGG -GATGGAAAAACTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTTATGA -AGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCA -GAATCTCGCAGGGAGCTGGATGGAGCTTAAGAGAAACAGCCTGCCTGGGCAAAGCTTACG -CCCAGATGTGGTCGCTTATGTACTTCCACAGAAGGGATCTGCGTTTAGCCTCCATGGCCA -TATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACG -CTCATCACCAGTGGATGACCACTGAAGATATGCTCAAAGTGTGGAACAGAGTGTGGATAG -AAGACAACCCTAATATGACTGACAAGACTCCAGTCCATTCGTGGGAAGATATACCTTACC -TAGGGAAAAGAGAGGATTTGTGGTGTGGATCCCTGATTGGACTTTCTTCCAGAGCCACCT -GGGCGAAGAACATTCATACGGCCATAACCCAGGTCAGGAACCTGATCGGAAAAGAGGAAT -ACGTGGATTACATGCCAGTAATGAAAAGATACAGTGCTCCTTCAGAGAGTGAAGGAGTTC -TGTAATTACCAACAACAAACACCAAAGGCTATTGAAGTCAGGCCACTTGTGCCACGGTTT -GAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAATGGGAGGCGTAATAATCCCCAGGGAG -GCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCT -CCCATCACTGATAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTG -GTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGG -GAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGAT -GGATTGGTGTTGTTGATCCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome +AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAGTTCTAACAGTTTGTTTAAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGGTGGTTAGACCGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAGGGTTGGTGAAGAGATTCTCAACCGGACTGTTTTCCGGGAAAGGACCCTTACGGATGGTGCTAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAAAGATGGGGACAGTTGAAGAAAAACAAGGCCATCAAGATACTGACTGGATTCAGGAAGGAGATAGGCCGCATGCTGAACATCTTGAACGGGAGAAAGAGGTCAACAATAACATTGCTATGCTTGATTCCCACCGTAATGGCATTCCACTTGTCAACAAGAGATGGCGAACCCCTTATGATAGTAGCAAAACACGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAAGGAATCAACAAATGCACTCTTATTGCCATGGACTTGGGTGAAATGTGTGAGGACACCGTCACGTATAAATGCCCTCTACTGGTCAACACCGAACCTGAAGACATTGATTGCTGGTGCAATCTCACGTCTACCTGGGTCATGTATGGGACATGTACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAGCTTTAACACCACATTCAGGAATGGGATTGGAAACAAGGGCTGAGACATGGATGTCATCGGAAGGGGCTTGGAAACATGCCCAGAGAGTGGAGAGCTGGATACTCAGAAACCCAGGATTCGCGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCTTCTTTGTTCTAATGATGCTGGTCGCTCCATCCTACGGAATGCGATGCGTAGGAGTGGGGAACAGAGATTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACACGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAATTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACTTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCCTGTTTGGAAAAGGAGGAGTTGTGACATGTGCAAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTGGTCCAAATTGAAAACCTTGAATACACAGTGGTTGTGACAGTCCACAATGGAGACACCCACGCAGTAGGAAATGACACATCCAACCATGGAGTGACAGCCACGATAACTCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCCGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTGCCATGGACAGCAGGAGCAGACACATCAGAAGTCCATTGGAATTATAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTAAAGTGCAAAGTACGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAGGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTACTGGAGCTCCATGCAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGCATCATTTCATCTACTCCTTTTGCTGAGAATACCAACAGTGTAACCAATATTGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTTAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGTGGACTGTTCACATCATTGGGAAAAGCTGTGCACCAGGTTTTTGGTAGTGTCTACACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATCGGCACGAACTCAAGAAACACTTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGTTTCACGGTTCAAGCAGACATGGGTTGTGTGGTGTCATGGAGTGGGAAAGAATTGAAATGTGGAAGTGGAATTTTTGTGATTGACAACGTGCACACTTGGACAGAACAGTACAAATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCCGCAATATTGAATGCCCACAAAGATGGGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAACAAATAACCAACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTGGTGGCCGGGGATGTGAAAGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCTCCAGTGAATGATTTGAAATATTCATGGAAGACATGGGGGAAAGCAAAAATCTTTACTCCAGAAGCAAGAAATAGCACATTCTTGATAGACGGACCAGACACCTCCGAATGCCCCAATGAACGAAGAGCATGGAACTTTCTTGAGGTAGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTTCGAGAAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCGGCAATCAAAGATCAGAAAGCCGTGCATGCTGACATGGGCTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAGAGAAAGCATCCCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACTCACACATTGTGGAGCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAAGCATATGCAGGCCCCTTTTCACAGCACAATTACCGCCAGGGCTATGCCACGCAGACCATGGGCCCATGGCACTTGGGCAAATTGGAAATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACCACAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAATTGGTCACACAGTGGTGCTGCCGCTCCTGCACGATGCCTCCCTTAAGGTTTTTGGGAGAGGATGGGTGTTGGTATGGGATGGAAATTAGGCCCTTAAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGTCGGCCGGACAGGGTTCATCAGAAACTTTTTCTATGGGGCTGTTATGTCTGACCCTGTTCATGGAAGAATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTGGTTGTGGTGACCACCCTTTGTGCCATCATCCTAGGAGGTCTCACGTGGATGGACTTACTACGAGCCATTATCATGTTAGGGGACACCATGTTTGGTAGAATGGGAGGACAGATTCACCTAGCCATCATGGCAGTGTTCAAGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAGCACTAATGGTGATAGGAATGGCCATGACAACGGTGTTTTCAATTCCACATGACCTTATGGAATTCATTGATGGAATATCATTGGGGCTAATCTTGCTGAAAATGGTAACACATTTTGACAACACCCAAGTGGGAACTTTAGCCCTTTCCTTAACTTTCATAAGATCAACAATGCCATTGATCATGGCTTGGAGGACCATCATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTATGTAGGACAAGCTGTCTTCAAAAGCAGTCCCACTGGGTAGAAATAACAGCAATCATCTTAGGAGCCCAGGCTCTGCCAGTGTACTTAATGACTCTCATGAAAGGAGCCTCAAAAAGATCTTGGCCTCTTAACGAGGGCATAATGGCTGTGGGCTTGGTCAGTCTCTTGGGAAGCGCCCTTCTAAAGAATGATGTCCCTTTGGCTGGTCCAATGGTGGCAGGAGGTTTACTTCTGGCAGCCTACGTGATGAGTGGTAGCTCAGCAGACCTGTCACTAGAGAAGGCCGCCAATGTGCAGTGGGATGAGATGGCAGACATAACAGGCTCAAGCCCAATCATAGAAGTGAAGCAGGATGAAGATGGCTCTTTCTCCATACGGGACGTCGAGGAAACCAACATGATAACCCTTTTGGTGAAACTGGCACTGATAACTGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACTTTATGGTACATGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTTCCCTCACCCGCTACCGCTCAGAAAGCCACACTGACTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTGTTTGGGAAAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAACAAGAGGATCAGTGATCTGCCATGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCAGGAACGACATGATATCATACGGTGGGGGATGGAGGCTCGGAGACAAATGGGACAAAGAAGAAGATGTTCAGGTCCTAGCCATAGAACCAGGAAAAAATCCGAAACATGTCCAAACGAAACCCGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTGGATTTCAAACCCGGAACATCTGGTTCTCCCATCATTAACAAGAAAGGAAAAGTTATCGGACTCTATGGAAATGGAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGTGAGCCAGATTATGAAGTGGATGAGGACATCTTTCGAAAGAAAAGATTAACCATAATGGACTTACACCCCGGAGCTGGCAAGACAAAAAGAATTCTCCCATCAATAGTCAGAGAAGCTCTAAAAAGGAGGCTGCGAACCCTGATTTTGGCTCCCACGAGAGTGGTGGCAGCCGAGATGGAAGAGGCCCTTCGCGGACTACCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAGGAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTCTTGTCATCAACCAGAGTTCCAAATTACAACCTCATAGTAATGGATGAAGCGCATTTCACAGACCCTTCTAGTGTCGCAGCTAGAGGATACATCTCAACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCTTCATGACTGCAACCCCTCCCGGAGCAACAGATCCCTTCCCCCAGAGCAACAGCCCAATAGAAGACATCGAGAGAGAAATTCCAGAAAGGTCATGGAATACAGGATTCGACTGGATAACAGACTACCAAGGGAAGACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAAATTGCTTGAGAAAGTCGGGAAAGAAGGTGATCCAGTTGAGTAGGAAAACCTTTGACACAGAGTATCCAAAAACGAAACTCACAGACTGGGATTTTGTGGTCACCACAGACATATCTGAAATGGGGGCCAATTTTAGAGCTGGGAGAGTGATAGACCCCAGGAGATGCCTCAAGCCAGTCATCCTAACAGATGGGCCAGAGAGAGTCATTTTGGCAGGTCCCATTCCAGTGACTCCAGCAAGCGCTGCTCAGAGAAGAGGGCGAATAGGTAGAAACCCAGCACAAGAAGACGACCAGTATGTCTTCTCTGGAGACCCATTGAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGATGCTGCTTGACAATATCTACACCCCGGAAGGGATCATTCCAACATTGTTTGGTCCGGAAAGGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTTTTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCAGCTGGTATTTCTTACAAAGACCGGGAATGGTGCTTCACAGGGGAAAGGAATAACCAAATTTTAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAACTAAGACCAAAATGGTTAGATGCACGTGTCTATGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGTTTGCTAGTGGAAGAAAGAGCATAACCCTTGACATCCTGACAGAGATTGCCAGCTTGCCAACTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGACAACATAGTCATGCTCCACACAACAGAAAGGGGAGGGAGGGCCTACCAACACGCCCTGAACGAACTCCCGGAGTCATTGGAAACACTCATGCTTGTAGCTTTATTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTTATGCAAGGAAAAGGGATAGGGAAACTGTCAATGGGTTTGATAGCTATTGCGGTAGCTAGTGGCTTACTCTGGGTAGCAGAAATTCAGCCCCAGTGGATAGCGGCCTCAATCATACTGGAGTTTTTTCTCATGGTGCTGTTGATACCAGAACCAGAAAAACAAAGGACCCCACAAGACAACCAGTTGATCTATGTCATACTGGCCATTCTCACCATTATTGGTCTCATAGCAGCCAACGAGATGGGGCTGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCCTCGATGTGGATTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACTATTCTGACTCCCATGCTGAGACACACCATAGAAAACACATCTGCCAACCTATCTCTGGCGGCCATTGCCAATCAAGCAGCTGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGGACCTTGGTGTGCCGCTGTTAGCAATGGGATGTTATTCTCAAGTGAACCCAACAACTTTGACAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGTCCAGGATTGCAGGCAAAAGCCACAAGAGAGGCTCAGAAAAGGACAGCTGCTGGGATCATGAAGAACCCCACGGTGGATGGAATAACAGTAATAGATCTAGAACCAATATCTTATGACCCAAAGTTTGAAAAGCAATTAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACATGGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAGTCTTAACTTTGTGGGAGGGCAACCCGGGAAGATTTTGGAACACGACTATAGCCGTATCCACTGCCAACATTTTCAGGGGAAGCTACTTGGCGGGAGCTGGACTGGCTTTCTCACTCATAAAGAATGCACAAACCCCCAGGAGGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCATTAGATAGGAAGGAGTTTGAAGAGTACAAGAGAAGTGGAATACTAGAAGTGGACAGGACTGAAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTGTCCAGAGGGTCCAGCAAGATCAGATGGATTGTTGAAAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTGGATCTTGGTTGCGGGAGAGGAGGATGGTCGTATTACATGGCGACACTCAAGAACGTGACTGAGGTGAAAGGGTACACGAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACCTATGGCTGGAATTTGGTCAAGCTCCATTCAGGGGTTGACGTGTTCTACAAACCCACTGAGCAAGTGGACACCCTGCTCTGTGATATTGGAGAGTCATCTTCTAATCCGACAATAGAGGAAGGAAGAACATTAAGAGTTCTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCATCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAACTGGAGAAACTGCAGAGAAAGCATGGTGGAAGTCTTATCAGATGCCCGCTATCCAGGAATTCCACTCATGAGATGTATTGGGTGTCAGGTGCGTCGGGAAACATCGTGAGCTCTGTGAACACAACATCAAAGATGCTGTTGAACAGGTTTACCACGAGGCATAGGAAACCCACCTATGAGAAGGACGTAGACCTTGGAGCAGGAACAAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAAGGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACTTGGCACTATGATCAGGAAAATCCATACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCAGCATCCTCCATGGTAAACGGGGTAGTAAAACTGCTGACAAAACCTTGGGACGTGATTCCAATGGTGACCCAGTTAGCCATGACAGACACAACCCCCTTTGGGCAACAAAGAGTGTTTAAAGAGAAGGTGGACACCAGAACACCACAACCAAAACCAGGCACACGAGTGGTTATGACCACAACAGCCAATTGGCTGTGGGCCCTCCTTGGGAGGAAGAAAAATCCCAGACTGTGCACGAGGGAAGAGTTCATCTCAAAAGTTAGGTCAAACGCAGCCATAGGTGCAGTCTTTCAGGAAGAACAGGGATGGACATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGGCTCTGCACCAGGAAGGGAAATGTGAATCGTGTGTCTACAACATGATGGGAAAACGTGAGAAAAAACTAGGAGAGTTTGGTAGAGCCAAAGGAAGCCGAGCAATCTGGTACATGTGGCTGGGAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTCTTAAATGAAGATCACTGGTTTGGCAGAGAAAATTCATGGAGTGGAGTGGAAGGAGAAGGTCTGCATAGATTGGGATACATCCTAGAGGACATAGACAAGAAGGATGGAGACCTGATGTATGCTGATGACACAGCAGGTTGGGACACAAGAATCACTGAAGATGACCTTCTAAATGAAGAACTGATCACGGAACAGATGGCCCCTCATCATAAGATCTTAGCCAAAGCCATTTTCAAACTAACTTATCAAAACAAAGTGGTAAAAGTCCTCAGACCCACACCGAAAGGAGCGGTGATGGACATCATATCCAGGAAAGACCAAAGAGGTAGTGGACAGGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTACAACTCATCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGCTGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTGAAGAGGATGGCAATCAGTGGAGATGATTGTGTGGTGAAGCCCCTGGATGAGAGGTTCAGCACTTCCCTCCTCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCCAAGGGATGGAAAAATTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTCATGAAGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCAGAATCTCGCAGGGGGCTGGATGGAGCTTAAAAGAAACAGCCTGTCTGGGCAAAGCTTACGCCCAGATGTGGTCGCTCATGTATTTTCACAGAAGGGACCTGCGTTTAGCCTCCATGGCCATATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACGCCCACCATCAGTGGATGACCACTGAAGACATGCTCAAAGTGTGGAACAGAGTGTGGATAGAAGACAACCCTAACATGACTGACAAAACTCCAGTCCATTCGTGGGAAGACATACCTTACCTAGGGAAAAGAGAGGATTTGTGGTGTGGATCCTTGATTGGACTTTCTTCCAGAGCCACCTGGGCGAAAAACATTCACACAGCCATAACCCAAGTCAGGAACCTGATCGGGAAAGAGGAGTATGTGGATTACATGCCAGTCATGAAAAGATACAGCGCTCCTTTCGAGAGTGAAGGAGTTCTGTAATTACCAACAACAAACACCAAAGCCTATTGAAGTCAGGCCACTTGTGCCACGGCTTGAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAACGGGAGGCGTAAAAATTCCCAGGGAGGCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCTCCCATCACTGACAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTGGTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGATGGATTGGTGTTGTTGATCCAACAGGTTCT diff --git a/nextclade/datasets/denv4/tree.json b/nextclade/datasets/denv4/tree.json index 6523f07f..a81a346d 100644 --- a/nextclade/datasets/denv4/tree.json +++ b/nextclade/datasets/denv4/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Real-time tracking of dengue virus evolution", "updated": "2024-05-25", "build_url": "https://github.com/nextstrain/dengue", "maintainers": [{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": true, "color_by": "clade_membership"}, "genome_annotations": {"nuc": {"end": 10649, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/config/reference_denv4_genome.gb"}, "2K": {"end": 6827, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 6759, "strand": "+", "type": "CDS"}, "C": {"end": 440, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 102, "strand": "+", "type": "CDS"}, "E": {"end": 2423, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 939, "strand": "+", "type": "CDS"}, "M": {"end": 938, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 441, "strand": "+", "type": "CDS"}, "NS1": {"end": 3479, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 2424, "strand": "+", "type": "CDS"}, "NS2A": {"end": 4133, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 3480, "strand": "+", "type": "CDS"}, "NS2B": {"end": 4523, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 4134, "strand": "+", "type": "CDS"}, "NS3": {"end": 6377, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 4524, "strand": "+", "type": "CDS"}, "NS4A": {"end": 6758, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 6378, "strand": "+", "type": "CDS"}, "NS4B": {"end": 7562, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 6828, "strand": "+", "type": "CDS"}, "NS5": {"end": 10262, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 7563, "strand": "+", "type": "CDS"}, "pr": {"end": 713, "seqid": "../phylogenetic/config/reference_denv4_genome.gb", "start": 441, "strand": "+", "type": "CDS"}}, "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Pakistan", "#5E1D9D"], ["India", "#531EA6"], ["Sri Lanka", "#4D22AE"], ["Myanmar", "#492AB5"], ["Thailand", "#4531BC"], ["Malaysia", "#4138C3"], ["Laos", "#4041C7"], ["Singapore", "#3F4ACA"], ["China", "#3F53CD"], ["Cambodia", "#3E5CD0"], ["Vietnam", "#4064CF"], ["Indonesia", "#416DCE"], ["Taiwan", "#447DCC"], ["Philippines", "#4784C8"], ["South Korea", "#4A8BC3"], ["Japan", "#4C91BF"], ["French Polynesia", "#4F97BA"], ["Australia", "#539CB4"], ["Kiribati", "#68AF93"], ["Senegal", "#72B485"], ["France", "#95BD60"], ["Paraguay", "#B5BD4C"], ["Bolivia", "#BBBC49"], ["Brazil", "#C1BA46"], ["Ecuador", "#CDB642"], ["Colombia", "#D1B340"], ["Venezuela", "#DBAC3D"], ["Nicaragua", "#E39B39"], ["El Salvador", "#E68D36"], ["Dominica", "#E67C33"], ["Jamaica", "#E5692F"], ["Dominican Republic", "#E35E2D"], ["Haiti", "#E1532B"], ["Mexico", "#E04929"], ["Cuba", "#DE3E27"], ["USA", "#DB2823"]]}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["Asia", "#447CCD"], ["Oceania", "#5EA9A1"], ["Africa", "#8ABB6A"], ["Europe", "#BEBB48"], ["South America", "#E29E39"], ["North America", "#E2562B"]]}, {"key": "genotype_nextclade", "title": "Dengue Genotype (Nextclade)", "type": "categorical", "scale": [["DENV4/I", "#4E94BD"], ["DENV4/II", "#81BA72"], ["DENV4/S", "#C8B944"]]}, {"key": "serotype_genbank", "title": "Serotype (Genbank metadata)", "type": "categorical", "scale": [["denv4", "#4C90C0"]]}, {"key": "clade_membership", "title": "Dengue Genotype (Nextstrain)", "type": "categorical"}], "filters": ["country", "region", 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["A2102G"]}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}, "root_sequence": {"nuc": "AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAGTTCTAACAGTTTGTTTGAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGGTGGTTAGACCACCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAGGGTTGGTGAAGAGATTCTCAACCGGACTTTTTTCTGGGAAAGGACCCTTACGGATGGTGCTAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAGAGATGGGGACAGTTGAAGAAAAATAAGGCCATCAAGATACTGATTGGATTCAGGAAGGAGATAGGCCGCATGCTGAACATCTTGAACGGGAGAAAAAGGTCAACGATAACATTGCTGTGCTTGATTCCCACCGTAATGGCGTTTTCCCTCAGCACAAGAGATGGCGAACCCCTCATGATAGTGGCAAAACATGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAATGCACTCTCATTGCCATGGACTTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCCCCCTACTGGTCAATACCGAACCTGAAGACATTGATTGCTGGTGCAACCTCACGTCTACCTGGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAGCTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGGATGTCATCGGAAGGGGCTTGGAAGCATGCTCAGAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCGCGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCTTCTTTGTCCTAATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTTAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCGAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCAGACATGGGTTGTGTGGCGTCATGGAGTGGGAAAGAATTGAAGTGTGGAAGCGGAATTTTTGTGGTTGACAACGTGCACACTTGGACAGAACAGTACAAATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCTGCAATATTAAATGCCCACAAAGATGGGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAGCAAATAACCAACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTAGTGGCTGGGGATGTGAAGGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCCCCAGTGAGTGATCTGAAATATTCATGGAAGACATGGGGAAAAGCAAAAATCTTCACCCCAGAAGCAAGAAATAGCACATTTTTAATAGACGGACCAGACACCTCTGAATGCCCCAATGAACGAAGAGCATGGAACTCTCTTGAGGTGGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTCCGAGAAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCTGCAATTAAAGATCAGAAAGCTGTGCATGCTGACATGGGTTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAGAGAAAGCATCTCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACCCACACACTGTGGAGCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAATCATATGCGGGCCCTTTTTCACAGCACAATTACCGCCAGGGCTATGCCACGCAAACCGTGGGCCCATGGCACTTAGGCAAATTAGAGATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACCATAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAACTAGTCACGCAATGGTGCTGCCGCTCCTGCACGATGCCTCCCTTAAGGTTCTTGGGAGAAGATGGGTGCTGGTATGGGATGGAGATTAGGCCCTTGAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGACGGCCGGACAGGGCACATCAGAAACTTTTTCTATGGGTCTGTTGTGCCTGACCTTGTTTGTGGAAGAATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTAGTTGTGGTGATCACTCTTTGTGCTATCATCCTGGGAGGCCTCACATGGATGGACTTACTACGAGCCCTCATCATGTTGGGGGACACTATGTCTGGTAGAATAGGAGGACAGATCCACCTAGCCATCATGGCAGTGTTCAAGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAGCACTAATGGTAATAGGAATGGCCATGACAACGGTGCTTTCAATTCCACATGACCTTATGGAACTCATTGATGGAATATCACTGGGACTAATTTTGCTAAAAATAGTAACACAGTTTGACAACACCCAAGTGGGAACCTTAGCTCTTTCCTTGACTTTCATAAGATCAACAATGCCATTGGTCATGGCTTGGAGGACCATTATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTGTGCAGGACAAGCTGTCTTCAAAAACAGTCTCATTGGGTAGAAATAACAGCACTCATCCTAGGAGCCCAAGCTCTGCCAGTGTACCTAATGACTCTTATGAAAGGAGCCTCAAGAAGATCTTGGCCTCTTAACGAGGGCATAATGGCTGTGGGTTTGGTTAGTCTCTTAGGAAGCGCTCTTTTAAAGAATGATGTCCCTTTAGCTGGCCCAATGGTGGCAGGAGGCTTACTTCTGGCGGCTTACGTGATGAGTGGTAGCTCAGCAGATCTGTCACTAGAGAAGGCCGCCAACGTGCAGTGGGATGAAATGGCAGACATAACAGGCTCAAGCCCAATCGTAGAAGTGAAGCAGGATGAAGATGGCTCTTTCTCCATACGGGACGTCGAGGAAACCAATATGATAACCCTTTTGGTGAAACTGGCACTGATAACAGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACCTTATGGTACATGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTCCCCTCACCCGCTGCCACTAAAAAAGCCGCACTGTCTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTATTCGGGAAAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAACAAGAGGATCAGTGATCTGCCACGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCAGGAATGACATGATATCATACGGTGGGGGATGGAGGCTTGGAGACAAATGGGACAAAGAAGAAGACGTTCAGGTCCTCGCCATAGAACCAGGAAAAAATCCTAAACATGTCCAAACGAAACCTGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTAGATTTCAAACCCGGAACGTCTGGTTCTCCCATCATCAACAGGAAAGGAAAAGTCATCGGACTCTATGGAAATGGAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGAGAGCCAGATTATGAAGTGGATGAGGACATTTTTCGAAAGAAAAGATTAACTATAATGGACTTACACCCCGGAGCTGGAAAGACAAAAAGAATTCTTCCATCAATAGTGAGAGAAGCCTTAAAAAGGAGGCTACGAACTTTGATTTTAGCTCCCACGAGAGTGGTGGCGGCCGAGATGGAAGAGGCCCTACGTGGACTGCCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAGGAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTTTTGTCATCAACCAGGGTTCCAAATTACAACCTTATAGTGATGGATGAAGCACATTTCACCGATCCTTCTAGTGTCGCGGCTAGAGGATACATCTCGACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCTTCATGACCGCAACCCCTCCCGGAGCGACAGATCCCTTTCCCCAGAGCAACAGCCCAATAGAAGACATCGAGAGGGAAATTCCGGAAAGGTCATGGAACACAGGGTTCGACTGGATAACAGACTACCAAGGGAAAACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAAATTGTTTGAGAAAGTCGGGAAAGAAAGTTATCCAGTTGAGTAGGAAAACCTTTGATACAGAGTATCCAAAAACGAAACTCACGGACTGGGACTTTGTGGTCACTACAGACATATCTGAAATGGGGGCCAATTTTAGAGCCGGGAGAGTGATAGACCCTAGAAGATGCCTCAAGCCAGTTATCCTACCAGATGGGCCAGAGAGAGTCATTTTAGCAGGTCCTATTCCAGTGACTCCAGCAAGCGCTGCTCAGAGAAGAGGGCGAATAGGAAGGAACCCAGCACAAGAAGACGACCAATACGTTTTCTCCGGAGACCCACTAAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGATGCTGCTTGACAATATCTACACCCCAGAAGGGATCATTCCAACATTGTTTGGTCCGGAAAGGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTTTTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCTGCTGGCATTTCTTACGAAGATCGGGAATGGTGCTTCACAGGGGAAAGAAATAACCAAATTTTAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAGCTAAGGCCAAGATGGTTAGATGCACGTGTATACGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGTTTGCCAGTGGAAGGAAGAGTATAACTCTCGACATCCTAACAGAGATTGCCAGTTTGCCAACTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGATAACATAGTCATGCTCCACACAACAGAAAGAGGAGGGAGGGCCTATCAACACGCCCTGAACGAACTTCCGGAGTCACTGGAAACACTCATGCTTGTAGCTTTACTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTCATGCAAGGGAAAGGAATAGGGAAATTGTCAATGGGTTTGATAACCATTGCGGTGGCTAGTGGCTTGCTCTGGGTAGCAGAAATTCAACCCCAGTGGATAGCGGCCTCAATCATACTAGAGTTTTTTCTCATGGTACTGTTGATACCGGAACCAGAAAAACAAAGGACCCCACAAGACAATCAATTGATCTACGTCATATTGACCATTCTCACCATCATTGGTCTAATAGCAGCCAACGAGATGGGGCTGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCCTCGATGTGGACTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACAATTCTGACTCCCATGCTGAGACACACCATAGAAAACACGTCGGCCAACCTATCTCTAGCAGCCATTGCCAACCAGGCAGCCGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGGACCTCGGTGTGCCGCTGTTAGCAATGGGATGCTATTCTCAAGTGAACCCAACAACCTTGACAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGCCCAGGATTGCAGGCAAAAGCCACAAGAGAGGCCCAGAAAAGGACAGCTGCTGGGATCATGAAAAATCCCACAGTGGACGGGATAACAGTAATAGATCTAGAACCAATATCCTATGACCCAAAATTTGAAAAGCAATTAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACATGGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAATCTTGACCTTGTGGGAGGGCAACCCGGGAAGGTTTTGGAACACGACCATAGCCGTATCCACCGCCAACATTTTCAGGGGAAGTTACTTGGCGGGAGCTGGACTGGCTTTTTCACTCATAAAGAATGCACAAACCCCTAGGAGGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCATTAGACAGAAAAGAGTTTGAAGAGTATAAAAGAAGTGGAATACTAGAAGTGGACAGGACTGAAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTATCAAGAGGGTCCAGTAAGATCAGATGGATTGTTGAGAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTAGATCTTGGCTGTGGGAGAGGAGGATGGTCTTATTACATGGCGACACTCAAGAACGTGACTGAAGTGAAAGGGTATACAAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACTTATGGTTGGAATTTGGTCAAACTCCATTCAGGGGTTGACGTGTTCTACAAACCCACAGAGCAAGTGGACACCCTGCTCTGTGATATTGGGGAGTCATCTTCTAATCCAACAATAGAGGAAGGAAGAACATTAAGAGTTTTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCATCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAGCTGGAGAAACTGCAGAGAAAACATGGTGGGAACCTTGTCAGATGCCCGCTGTCCAGGAACTCCACCCATGAGATGTATTGGGTGTCAGGAGCGTCGGGAAACATTGTGAGCTCTGTGAACACAACATCAAAGATGTTGTTGAACAGGTTCACAACAAGGCATAGGAAACCCACTTATGAGAAGGACGTAGATCTTGGGGCAGGAACGAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAAGGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACCTGGCATTATGATCAGGAAAACCCATACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCTGCATCCTCCATGGTGAACGGGGTGGTAAAACTGCTAACAAAACCCTGGGATGTGATTCCAATGGTGACTCAGTTAGCCATGACAGATACAACCCCTTTTGGGCAACAAAGAGTGTTCAAAGAGAAGGTGGATACCAGAACACCACAACCAAAACCCGGTACACGAATGGTTATGACCACGACAGCCAATTGGCTGTGGGCCCTCCTTGGAAAGAAGAAAAATCCCAGACTGTGCACAAGGGAAGAGTTCATCTCAAAAGTTAGATCAAACGCAGCCATAGGCGCAGTCTTTCAGGAAGAACAGGGATGGACATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGGCCCTACACCAGGAAGGGAAATGTGAATCGTGTGTCTATAACATGATGGGAAAACGTGAGAAAAAGTTAGGAGAGTTTGGCAGAGCCAAGGGAAGCCGAGCAATCTGGTACATGTGGCTGGGAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTTTTGAATGAAGATCACTGGTTTGGCAGAGAAAATTCATGGAGTGGAGTGGAAGGGGAAGGTCTGCACAGATTGGGATATATCCTGGAGGAGATAGACAAGAAGGATGGAGACCTAATGTATGCTGATGACACAGCAGGCTGGGACACAAGAATCACTGAGGATGACCTTCAAAATGAGGAACTGATCACGGAACAGATGGCTCCCCACCACAAGATCCTAGCCAAAGCCATTTTCAAACTAACCTATCAAAACAAAGTGGTGAAAGTCCTCAGACCCACACCGCGGGGAGCGGTGATGGATATCATATCCAGGAAAGACCAAAGAGGTAGTGGACAAGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTTCAACTCATCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGTTGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTAAAGAGGATGGCAATCAGTGGAGACGATTGCGTGGTGAAGCCCCTAGATGAGAGGTTTGGCACTTCCCTCCTCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCTAAGGGATGGAAAAACTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTTATGAAGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCAGAATCTCGCAGGGAGCTGGATGGAGCTTAAGAGAAACAGCCTGCCTGGGCAAAGCTTACGCCCAGATGTGGTCGCTTATGTACTTCCACAGAAGGGATCTGCGTTTAGCCTCCATGGCCATATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACGCTCATCACCAGTGGATGACCACTGAAGATATGCTCAAAGTGTGGAACAGAGTGTGGATAGAAGACAACCCTAATATGACTGACAAGACTCCAGTCCATTCGTGGGAAGATATACCTTACCTAGGGAAAAGAGAGGATTTGTGGTGTGGATCCCTGATTGGACTTTCTTCCAGAGCCACCTGGGCGAAGAACATTCATACGGCCATAACCCAGGTCAGGAACCTGATCGGAAAAGAGGAATACGTGGATTACATGCCAGTAATGAAAAGATACAGTGCTCCTTCAGAGAGTGAAGGAGTTCTGTAATTACCAACAACAAACACCAAAGGCTATTGAAGTCAGGCCACTTGTGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAATGGGAGGCGTAATAATCCCCAGGGAGGCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCTCCCATCACTGATAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTGGTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGATGGATTGGTGTTGTTGATCCAACAGGTTCT", "2K": "TPQDNQLIYVILTILTIIGLIAA", "C": "MNQRKKVVRPPFNMLKRERNRVSTPQGLVKRFSTGLFSGKGPLRMVLAFITFLRVLSIPPTAGILKRWGQLKKNKAIKILIGFRKEIGRMLNILNGRKRSTITLLCLIPTVMA", "E": "MRCVGVGNRDFVEGVSGGAWVDLVLEHGGCVTTMAQGKPTLDFELTKTTAKEVALLRTYCIEASISNITTATRCPTQGEPYLKEEQDQQYICRRDVVDRGWGNGCGLFGKGGVVTCAKFSCSGKITGNLVQIENLEYTVVVTVHNGDTHAVGNDTSNHGVTAMITPRSPSVEVKLPDYGELTLDCEPRSGIDFNEMILMKMKKKTWLVHKQWFLDLPLPWTAGADTSEVHWNYKERMVTFKVPHAKRQDVTVLGSQEGAMHSALAGATEVDSGDGNHMFAGHLKCKVRMEKLRIKGMSYTMCSGKFSIDKEMAETQHGTTVVKVKYEGAGAPCKVPIEIRDVNKEKVVGRIISSTPLAENTNSVTNIELEPPFGDSYIVIGVGNSALTLHWFRKGSSIGKMFESTYRGAKRMAILGETAWDFGSVGGLFTSLGKAVHQVFGSVYTTMFGGVSWMIRILIGFLVLWIGTNSRNTSMAMTCIAVGGITLFLGFTVQA", "M": "FSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVTYKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSGMGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQRTVFFVLMMLVAPSYG", "NS1": "DMGCVASWSGKELKCGSGIFVVDNVHTWTEQYKFQPESPARLASAILNAHKDGVCGIRSTTRLENVMWKQITNELNYVLWEGGHDLTVVAGDVKGVLTKGKRALTPPVSDLKYSWKTWGKAKIFTPEARNSTFLIDGPDTSECPNERRAWNSLEVEDYGFGMFTTNIWMKFREGSSEVCDHRLMSAAIKDQKAVHADMGYWIESSKNQTWQIEKASLIEVKTCLWPKTHTLWSNGVLESQMLIPKSYAGPFSQHNYRQGYATQTVGPWHLGKLEIDFGECPGTTVTIQEDCDHRGPSLRTTTASGKLVTQWCCRSCTMPPLRFLGEDGCWYGMEIRPLSEKEENMVKSQVTA", "NS2A": "GQGTSETFSMGLLCLTLFVEECLRRRVTRKHMILVVVITLCAIILGGLTWMDLLRALIMLGDTMSGRIGGQIHLAIMAVFKMSPGYVLGVFLRKLTSRETALMVIGMAMTTVLSIPHDLMELIDGISLGLILLKIVTQFDNTQVGTLALSLTFIRSTMPLVMAWRTIMAVLFVVTLIPLCRTSCLQKQSHWVEITALILGAQALPVYLMTLMKGASRR", "NS2B": "SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSADLSLEKAANVQWDEMADITGSSPIVEVKQDEDGSFSIRDVEETNMITLLVKLALITVSGLYPLAIPVTMTLWYMWQVKTQR", "NS3": "SGALWDVPSPAATKKAALSEGVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMISYGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTSGSPIINRKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPSSVAARGYISTRVEMGEAAAIFMTATPPGATDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILPDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYEDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPRWLDARVYADPMALKDFKEFASGRK", "NS4A": "SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPESLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEIQPQWIAASIILEFFLMVLLIPEPEKQR", "NS4B": "NEMGLIEKTKTDFGFYQVKTETTILDVDLRPASAWTLYAVATTILTPMLRHTIENTSANLSLAAIANQAAVLMGLGKGWPLHRMDLGVPLLAMGCYSQVNPTTLTASLVMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYDPKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPILTLWEGNPGRFWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRR", "NS5": "GTGTTGETLGEKWKRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSSKIRWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGPGHEEPIPMATYGWNLVKLHSGVDVFYKPTEQVDTLLCDIGESSSNPTIEEGRTLRVLKMVEPWLSSKPEFCIKVLNPYMPTVIEELEKLQRKHGGNLVRCPLSRNSTHEMYWVSGASGNIVSSVNTTSKMLLNRFTTRHRKPTYEKDVDLGAGTRSVSTETEKPDMTIIGRRLQRLQEEHKETWHYDQENPYRTWAYHGSYEAPSTGSASSMVNGVVKLLTKPWDVIPMVTQLAMTDTTPFGQQRVFKEKVDTRTPQPKPGTRMVMTTTANWLWALLGKKKNPRLCTREEFISKVRSNAAIGAVFQEEQGWTSASEAVNDSRFWELVDKERALHQEGKCESCVYNMMGKREKKLGEFGRAKGSRAIWYMWLGARFLEFEALGFLNEDHWFGRENSWSGVEGEGLHRLGYILEEIDKKDGDLMYADDTAGWDTRITEDDLQNEELITEQMAPHHKILAKAIFKLTYQNKVVKVLRPTPRGAVMDIISRKDQRGSGQVGTYGLNTFTNMEVQLIRQMEAEGVITQDDMQNPKGLKERVEKWLKECGVDRLKRMAISGDDCVVKPLDERFGTSLLFLNDMGKVRKDIPQWEPSKGWKNWQEVPFCSHHFHKIFMKDGRSLVVPCRNQDELIGRARISQGAGWSLRETACLGKAYAQMWSLMYFHRRDLRLASMAICSAVPTEWFPTSRTTWSIHAHHQWMTTEDMLKVWNRVWIEDNPNMTDKTPVHSWEDIPYLGKREDLWCGSLIGLSSRATWAKNIHTAITQVRNLIGKEEYVDYMPVMKRYSAPSESEGVL", "pr": "FSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVTYKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKR"}} \ No newline at end of file +{"version": "v2", "meta": {"title": "Real-time tracking of dengue virus evolution", "updated": "2024-06-04", "build_url": "https://github.com/nextstrain/dengue", "maintainers": [{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": true, "color_by": "clade_membership"}, "genome_annotations": {"nuc": {"end": 10649, "start": 1, "strand": "+", "type": "##sequence-region pragma", "seqid": "resources/denv4/genome_annotation.gff3"}, "2K": {"end": 6827, "seqid": "resources/denv4/genome_annotation.gff3", "start": 6759, "strand": "+", "type": "gene"}, "C": {"end": 440, "seqid": "resources/denv4/genome_annotation.gff3", "start": 102, "strand": "+", "type": "gene"}, "E": {"end": 2423, "seqid": "resources/denv4/genome_annotation.gff3", "start": 939, "strand": "+", "type": "gene"}, "M": {"end": 938, "seqid": 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{"value": "MN448995"}, "author": {"author": "Berry,I.M.", "value": "Berry,I.M."}, "genotype_nextclade": {"value": "DENV4/I", "confidence": {"DENV4/I": 1.0}, "entropy": -1.000088900581841e-12}, "clade_membership": {"value": "DENV4/I"}, "region": {"value": "Asia", "confidence": {"Asia": 0.9999999999999999}, "entropy": -9.99866855976916e-13}, "serotype_genbank": {"value": "denv4"}, "country": {"value": "Thailand", "confidence": {"Thailand": 1.0}, "entropy": -1.000088900581841e-12}}, "branch_attrs": {"mutations": {"nuc": ["A2102G"]}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}, "root_sequence": {"nuc": "AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAGTTCTAACAGTTTGTTTAAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGGTGGTTAGACCGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAGGGTTGGTGAAGAGATTCTCAACCGGACTGTTTTCCGGGAAAGGACCCTTACGGATGGTGCTAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAAAGATGGGGACAGTTGAAGAAAAACAAGGCCATCAAGATACTGACTGGATTCAGGAAGGAGATAGGCCGCATGCTGAACATCTTGAACGGGAGAAAGAGGTCAACAATAACATTGCTATGCTTGATTCCCACCGTAATGGCATTCCACTTGTCAACAAGAGATGGCGAACCCCTTATGATAGTAGCAAAACACGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAAGGAATCAACAAATGCACTCTTATTGCCATGGACTTGGGTGAAATGTGTGAGGACACCGTCACGTATAAATGCCCTCTACTGGTCAACACCGAACCTGAAGACATTGATTGCTGGTGCAATCTCACGTCTACCTGGGTCATGTATGGGACATGTACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAGCTTTAACACCACATTCAGGAATGGGATTGGAAACAAGGGCTGAGACATGGATGTCATCGGAAGGGGCTTGGAAACATGCCCAGAGAGTGGAGAGCTGGATACTCAGAAACCCAGGATTCGCGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCTTCTTTGTTCTAATGATGCTGGTCGCTCCATCCTACGGAATGCGATGCGTAGGAGTGGGGAACAGAGATTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACACGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAATTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACTTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCCTGTTTGGAAAAGGAGGAGTTGTGACATGTGCAAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTGGTCCAAATTGAAAACCTTGAATACACAGTGGTTGTGACAGTCCACAATGGAGACACCCACGCAGTAGGAAATGACACATCCAACCATGGAGTGACAGCCACGATAACTCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCCGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTGCCATGGACAGCAGGAGCAGACACATCAGAAGTCCATTGGAATTATAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTAAAGTGCAAAGTACGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAGGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTACTGGAGCTCCATGCAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGCATCATTTCATCTACTCCTTTTGCTGAGAATACCAACAGTGTAACCAATATTGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTTAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGTGGACTGTTCACATCATTGGGAAAAGCTGTGCACCAGGTTTTTGGTAGTGTCTACACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATCGGCACGAACTCAAGAAACACTTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGTTTCACGGTTCAAGCAGACATGGGTTGTGTGGTGTCATGGAGTGGGAAAGAATTGAAATGTGGAAGTGGAATTTTTGTGATTGACAACGTGCACACTTGGACAGAACAGTACAAATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCCGCAATATTGAATGCCCACAAAGATGGGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAACAAATAACCAACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTGGTGGCCGGGGATGTGAAAGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCTCCAGTGAATGATTTGAAATATTCATGGAAGACATGGGGGAAAGCAAAAATCTTTACTCCAGAAGCAAGAAATAGCACATTCTTGATAGACGGACCAGACACCTCCGAATGCCCCAATGAACGAAGAGCATGGAACTTTCTTGAGGTAGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTTCGAGAAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCGGCAATCAAAGATCAGAAAGCCGTGCATGCTGACATGGGCTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAGAGAAAGCATCCCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACTCACACATTGTGGAGCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAAGCATATGCAGGCCCCTTTTCACAGCACAATTACCGCCAGGGCTATGCCACGCAGACCATGGGCCCATGGCACTTGGGCAAATTGGAAATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACCACAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAATTGGTCACACAGTGGTGCTGCCGCTCCTGCACGATGCCTCCCTTAAGGTTTTTGGGAGAGGATGGGTGTTGGTATGGGATGGAAATTAGGCCCTTAAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGTCGGCCGGACAGGGTTCATCAGAAACTTTTTCTATGGGGCTGTTATGTCTGACCCTGTTCATGGAAGAATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTGGTTGTGGTGACCACCCTTTGTGCCATCATCCTAGGAGGTCTCACGTGGATGGACTTACTACGAGCCATTATCATGTTAGGGGACACCATGTTTGGTAGAATGGGAGGACAGATTCACCTAGCCATCATGGCAGTGTTCAAGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAGCACTAATGGTGATAGGAATGGCCATGACAACGGTGTTTTCAATTCCACATGACCTTATGGAATTCATTGATGGAATATCATTGGGGCTAATCTTGCTGAAAATGGTAACACATTTTGACAACACCCAAGTGGGAACTTTAGCCCTTTCCTTAACTTTCATAAGATCAACAATGCCATTGATCATGGCTTGGAGGACCATCATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTATGTAGGACAAGCTGTCTTCAAAAGCAGTCCCACTGGGTAGAAATAACAGCAATCATCTTAGGAGCCCAGGCTCTGCCAGTGTACTTAATGACTCTCATGAAAGGAGCCTCAAAAAGATCTTGGCCTCTTAACGAGGGCATAATGGCTGTGGGCTTGGTCAGTCTCTTGGGAAGCGCCCTTCTAAAGAATGATGTCCCTTTGGCTGGTCCAATGGTGGCAGGAGGTTTACTTCTGGCAGCCTACGTGATGAGTGGTAGCTCAGCAGACCTGTCACTAGAGAAGGCCGCCAATGTGCAGTGGGATGAGATGGCAGACATAACAGGCTCAAGCCCAATCATAGAAGTGAAGCAGGATGAAGATGGCTCTTTCTCCATACGGGACGTCGAGGAAACCAACATGATAACCCTTTTGGTGAAACTGGCACTGATAACTGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACTTTATGGTACATGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTTCCCTCACCCGCTACCGCTCAGAAAGCCACACTGACTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTGTTTGGGAAAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAACAAGAGGATCAGTGATCTGCCATGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCAGGAACGACATGATATCATACGGTGGGGGATGGAGGCTCGGAGACAAATGGGACAAAGAAGAAGATGTTCAGGTCCTAGCCATAGAACCAGGAAAAAATCCGAAACATGTCCAAACGAAACCCGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTGGATTTCAAACCCGGAACATCTGGTTCTCCCATCATTAACAAGAAAGGAAAAGTTATCGGACTCTATGGAAATGGAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGTGAGCCAGATTATGAAGTGGATGAGGACATCTTTCGAAAGAAAAGATTAACCATAATGGACTTACACCCCGGAGCTGGCAAGACAAAAAGAATTCTCCCATCAATAGTCAGAGAAGCTCTAAAAAGGAGGCTGCGAACCCTGATTTTGGCTCCCACGAGAGTGGTGGCAGCCGAGATGGAAGAGGCCCTTCGCGGACTACCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAGGAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTCTTGTCATCAACCAGAGTTCCAAATTACAACCTCATAGTAATGGATGAAGCGCATTTCACAGACCCTTCTAGTGTCGCAGCTAGAGGATACATCTCAACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCTTCATGACTGCAACCCCTCCCGGAGCAACAGATCCCTTCCCCCAGAGCAACAGCCCAATAGAAGACATCGAGAGAGAAATTCCAGAAAGGTCATGGAATACAGGATTCGACTGGATAACAGACTACCAAGGGAAGACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAAATTGCTTGAGAAAGTCGGGAAAGAAGGTGATCCAGTTGAGTAGGAAAACCTTTGACACAGAGTATCCAAAAACGAAACTCACAGACTGGGATTTTGTGGTCACCACAGACATATCTGAAATGGGGGCCAATTTTAGAGCTGGGAGAGTGATAGACCCCAGGAGATGCCTCAAGCCAGTCATCCTAACAGATGGGCCAGAGAGAGTCATTTTGGCAGGTCCCATTCCAGTGACTCCAGCAAGCGCTGCTCAGAGAAGAGGGCGAATAGGTAGAAACCCAGCACAAGAAGACGACCAGTATGTCTTCTCTGGAGACCCATTGAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGATGCTGCTTGACAATATCTACACCCCGGAAGGGATCATTCCAACATTGTTTGGTCCGGAAAGGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTTTTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCAGCTGGTATTTCTTACAAAGACCGGGAATGGTGCTTCACAGGGGAAAGGAATAACCAAATTTTAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAACTAAGACCAAAATGGTTAGATGCACGTGTCTATGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGTTTGCTAGTGGAAGAAAGAGCATAACCCTTGACATCCTGACAGAGATTGCCAGCTTGCCAACTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGACAACATAGTCATGCTCCACACAACAGAAAGGGGAGGGAGGGCCTACCAACACGCCCTGAACGAACTCCCGGAGTCATTGGAAACACTCATGCTTGTAGCTTTATTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTTATGCAAGGAAAAGGGATAGGGAAACTGTCAATGGGTTTGATAGCTATTGCGGTAGCTAGTGGCTTACTCTGGGTAGCAGAAATTCAGCCCCAGTGGATAGCGGCCTCAATCATACTGGAGTTTTTTCTCATGGTGCTGTTGATACCAGAACCAGAAAAACAAAGGACCCCACAAGACAACCAGTTGATCTATGTCATACTGGCCATTCTCACCATTATTGGTCTCATAGCAGCCAACGAGATGGGGCTGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCCTCGATGTGGATTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACTATTCTGACTCCCATGCTGAGACACACCATAGAAAACACATCTGCCAACCTATCTCTGGCGGCCATTGCCAATCAAGCAGCTGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGGACCTTGGTGTGCCGCTGTTAGCAATGGGATGTTATTCTCAAGTGAACCCAACAACTTTGACAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGTCCAGGATTGCAGGCAAAAGCCACAAGAGAGGCTCAGAAAAGGACAGCTGCTGGGATCATGAAGAACCCCACGGTGGATGGAATAACAGTAATAGATCTAGAACCAATATCTTATGACCCAAAGTTTGAAAAGCAATTAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACATGGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAGTCTTAACTTTGTGGGAGGGCAACCCGGGAAGATTTTGGAACACGACTATAGCCGTATCCACTGCCAACATTTTCAGGGGAAGCTACTTGGCGGGAGCTGGACTGGCTTTCTCACTCATAAAGAATGCACAAACCCCCAGGAGGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCATTAGATAGGAAGGAGTTTGAAGAGTACAAGAGAAGTGGAATACTAGAAGTGGACAGGACTGAAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTGTCCAGAGGGTCCAGCAAGATCAGATGGATTGTTGAAAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTGGATCTTGGTTGCGGGAGAGGAGGATGGTCGTATTACATGGCGACACTCAAGAACGTGACTGAGGTGAAAGGGTACACGAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACCTATGGCTGGAATTTGGTCAAGCTCCATTCAGGGGTTGACGTGTTCTACAAACCCACTGAGCAAGTGGACACCCTGCTCTGTGATATTGGAGAGTCATCTTCTAATCCGACAATAGAGGAAGGAAGAACATTAAGAGTTCTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCATCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAACTGGAGAAACTGCAGAGAAAGCATGGTGGAAGTCTTATCAGATGCCCGCTATCCAGGAATTCCACTCATGAGATGTATTGGGTGTCAGGTGCGTCGGGAAACATCGTGAGCTCTGTGAACACAACATCAAAGATGCTGTTGAACAGGTTTACCACGAGGCATAGGAAACCCACCTATGAGAAGGACGTAGACCTTGGAGCAGGAACAAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAAGGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACTTGGCACTATGATCAGGAAAATCCATACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCAGCATCCTCCATGGTAAACGGGGTAGTAAAACTGCTGACAAAACCTTGGGACGTGATTCCAATGGTGACCCAGTTAGCCATGACAGACACAACCCCCTTTGGGCAACAAAGAGTGTTTAAAGAGAAGGTGGACACCAGAACACCACAACCAAAACCAGGCACACGAGTGGTTATGACCACAACAGCCAATTGGCTGTGGGCCCTCCTTGGGAGGAAGAAAAATCCCAGACTGTGCACGAGGGAAGAGTTCATCTCAAAAGTTAGGTCAAACGCAGCCATAGGTGCAGTCTTTCAGGAAGAACAGGGATGGACATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGGCTCTGCACCAGGAAGGGAAATGTGAATCGTGTGTCTACAACATGATGGGAAAACGTGAGAAAAAACTAGGAGAGTTTGGTAGAGCCAAAGGAAGCCGAGCAATCTGGTACATGTGGCTGGGAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTCTTAAATGAAGATCACTGGTTTGGCAGAGAAAATTCATGGAGTGGAGTGGAAGGAGAAGGTCTGCATAGATTGGGATACATCCTAGAGGACATAGACAAGAAGGATGGAGACCTGATGTATGCTGATGACACAGCAGGTTGGGACACAAGAATCACTGAAGATGACCTTCTAAATGAAGAACTGATCACGGAACAGATGGCCCCTCATCATAAGATCTTAGCCAAAGCCATTTTCAAACTAACTTATCAAAACAAAGTGGTAAAAGTCCTCAGACCCACACCGAAAGGAGCGGTGATGGACATCATATCCAGGAAAGACCAAAGAGGTAGTGGACAGGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTACAACTCATCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGCTGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTGAAGAGGATGGCAATCAGTGGAGATGATTGTGTGGTGAAGCCCCTGGATGAGAGGTTCAGCACTTCCCTCCTCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCCAAGGGATGGAAAAATTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTCATGAAGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCAGAATCTCGCAGGGGGCTGGATGGAGCTTAAAAGAAACAGCCTGTCTGGGCAAAGCTTACGCCCAGATGTGGTCGCTCATGTATTTTCACAGAAGGGACCTGCGTTTAGCCTCCATGGCCATATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACGCCCACCATCAGTGGATGACCACTGAAGACATGCTCAAAGTGTGGAACAGAGTGTGGATAGAAGACAACCCTAACATGACTGACAAAACTCCAGTCCATTCGTGGGAAGACATACCTTACCTAGGGAAAAGAGAGGATTTGTGGTGTGGATCCTTGATTGGACTTTCTTCCAGAGCCACCTGGGCGAAAAACATTCACACAGCCATAACCCAAGTCAGGAACCTGATCGGGAAAGAGGAGTATGTGGATTACATGCCAGTCATGAAAAGATACAGCGCTCCTTTCGAGAGTGAAGGAGTTCTGTAATTACCAACAACAAACACCAAAGCCTATTGAAGTCAGGCCACTTGTGCCACGGCTTGAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAACGGGAGGCGTAAAAATTCCCAGGGAGGCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCTCCCATCACTGACAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTGGTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGATGGATTGGTGTTGTTGATCCAACAGGTTCT", "2K": "TPQDNQLIYVILAILTIIGLIAA", "C": "MNQRKKVVRPPFNMLKRERNRVSTPQGLVKRFSTGLFSGKGPLRMVLAFITFLRVLSIPPTAGILKRWGQLKKNKAIKILTGFRKEIGRMLNILNGRKRSTITLLCLIPTVMA", "E": "MRCVGVGNRDFVEGVSGGAWVDLVLEHGGCVTTMAQGKPTLDFELIKTTAKEVALLRTYCIEASISNITTATRCPTQGEPYLKEEQDQQYICRRDVVDRGWGNGCGLFGKGGVVTCAKFSCSGKITGNLVQIENLEYTVVVTVHNGDTHAVGNDTSNHGVTATITPRSPSVEVKLPDYGELTLDCEPRSGIDFNEMILMKMKKKTWLVHKQWFLDLPLPWTAGADTSEVHWNYKERMVTFKVPHAKRQDVTVLGSQEGAMHSALTGATEVDSGDGNHMFAGHLKCKVRMEKLRIKGMSYTMCSGKFSIDKEMAETQHGTTVVKVKYEGTGAPCKVPIEIRDVNKEKVVGRIISSTPFAENTNSVTNIELEPPFGDSYIVIGVGDSALTLHWFRKGSSIGKMFESTYRGAKRMAILGETAWDFGSVGGLFTSLGKAVHQVFGSVYTTMFGGVSWMVRILIGFLVLWIGTNSRNTSMAMTCIAVGGITLFLGFTVQA", "M": "FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVTYKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSGMGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQRTVFFVLMMLVAPSYG", "NS1": "DMGCVVSWSGKELKCGSGIFVIDNVHTWTEQYKFQPESPARLASAILNAHKDGVCGIRSTTRLENVMWKQITNELNYVLWEGGHDLTVVAGDVKGVLTKGKRALTPPVNDLKYSWKTWGKAKIFTPEARNSTFLIDGPDTSECPNERRAWNFLEVEDYGFGMFTTNIWMKFREGSSEVCDHRLMSAAIKDQKAVHADMGYWIESSKNQTWQIEKASLIEVKTCLWPKTHTLWSNGVLESQMLIPKAYAGPFSQHNYRQGYATQTMGPWHLGKLEIDFGECPGTTVTIQEDCDHRGPSLRTTTASGKLVTQWCCRSCTMPPLRFLGEDGCWYGMEIRPLSEKEENMVKSQVSA", "NS2A": "GQGSSETFSMGLLCLTLFMEECLRRRVTRKHMILVVVTTLCAIILGGLTWMDLLRAIIMLGDTMFGRMGGQIHLAIMAVFKMSPGYVLGVFLRKLTSRETALMVIGMAMTTVFSIPHDLMEFIDGISLGLILLKMVTHFDNTQVGTLALSLTFIRSTMPLIMAWRTIMAVLFVVTLIPLCRTSCLQKQSHWVEITAIILGAQALPVYLMTLMKGASKR", "NS2B": "SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSADLSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMITLLVKLALITVSGLYPLAIPVTMTLWYMWQVKTQR", "NS3": "SGALWDVPSPATAQKATLTEGVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMISYGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTSGSPIINKKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPSSVAARGYISTRVEMGEAAAIFMTATPPGATDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDLPVWLSYKVASAGISYKDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPKWLDARVYADPMALKDFKEFASGRK", "NS4A": "SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPESLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGLLWVAEIQPQWIAASIILEFFLMVLLIPEPEKQR", "NS4B": "NEMGLIEKTKTDFGFYQVKTETTILDVDLRPASAWTLYAVATTILTPMLRHTIENTSANLSLAAIANQAAVLMGLGKGWPLHRMDLGVPLLAMGCYSQVNPTTLTASLVMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYDPKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPVLTLWEGNPGRFWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRR", "NS5": "GTGTTGETLGEKWKRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSSKIRWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGPGHEEPIPMATYGWNLVKLHSGVDVFYKPTEQVDTLLCDIGESSSNPTIEEGRTLRVLKMVEPWLSSKPEFCIKVLNPYMPTVIEELEKLQRKHGGSLIRCPLSRNSTHEMYWVSGASGNIVSSVNTTSKMLLNRFTTRHRKPTYEKDVDLGAGTRSVSTETEKPDMTIIGRRLQRLQEEHKETWHYDQENPYRTWAYHGSYEAPSTGSASSMVNGVVKLLTKPWDVIPMVTQLAMTDTTPFGQQRVFKEKVDTRTPQPKPGTRVVMTTTANWLWALLGRKKNPRLCTREEFISKVRSNAAIGAVFQEEQGWTSASEAVNDSRFWELVDKERALHQEGKCESCVYNMMGKREKKLGEFGRAKGSRAIWYMWLGARFLEFEALGFLNEDHWFGRENSWSGVEGEGLHRLGYILEDIDKKDGDLMYADDTAGWDTRITEDDLLNEELITEQMAPHHKILAKAIFKLTYQNKVVKVLRPTPKGAVMDIISRKDQRGSGQVGTYGLNTFTNMEVQLIRQMEAEGVITQDDMQNPKGLKERVEKWLKECGVDRLKRMAISGDDCVVKPLDERFSTSLLFLNDMGKVRKDIPQWEPSKGWKNWQEVPFCSHHFHKIFMKDGRSLVVPCRNQDELIGRARISQGAGWSLKETACLGKAYAQMWSLMYFHRRDLRLASMAICSAVPTEWFPTSRTTWSIHAHHQWMTTEDMLKVWNRVWIEDNPNMTDKTPVHSWEDIPYLGKREDLWCGSLIGLSSRATWAKNIHTAITQVRNLIGKEEYVDYMPVMKRYSAPFESEGVL", "pr": "FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVTYKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKR"}} \ No newline at end of file diff --git a/nextclade/resources/all/README.md b/nextclade/resources/all/README.md index cc205180..affdf57a 100644 --- a/nextclade/resources/all/README.md +++ b/nextclade/resources/all/README.md @@ -1,7 +1,26 @@ -# Nextclade dataset for "Dengue Virus" +# De dataset -## Dataset attributes +| Key | Value | +| :-- | :-- | +| name | Dengue (serotype-level) | +| authors | [Nextstrain](https://nextstrain.org) | +| reference | NC_002640.1 | +| workflow | https://github.com/nextstrain/dengue/tree/main/nextclade | +| path | `nextstrain/dengue/all` | -Nextclade dataset -Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html +## Scope of this dataset + +This dataset assigns serotype to dengue samples based on [criteria outlined by the WHO](https://pubmed.ncbi.nlm.nih.gov/26868382/) and tree placement nearest references [NC_001477.1 (DENV1)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001477.1), [NC_001474.2 (DENV2)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001474.2), [NC_001475.2 (DENV3)](https://www.ncbi.nlm.nih.gov/nuccore/NC_001475.2), and [NC_002640.1 (DENV4)](https://www.ncbi.nlm.nih.gov/nuccore/NC_002640.1). + +## Features + +This dataset supports: + +- Assignment of serotypes +- Phylogenetic placement +- Sequence quality control (QC) + +## What are Nextclade datasets + +Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/nextclade/resources/all/genome_annotation.gff3 b/nextclade/resources/all/genome_annotation.gff3 index a417d706..3d63959e 100644 --- a/nextclade/resources/all/genome_annotation.gff3 +++ b/nextclade/resources/all/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_002640.1 1 10649 -NC_002640.1 feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; -NC_002640.1 feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; -NC_002640.1 feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; -NC_002640.1 feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; -NC_002640.1 feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_002640.1 feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_002640.1 feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_002640.1 feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_002640.1 feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_002640.1 feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; -NC_002640.1 feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_002640.1 feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome 1 10649 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/resources/all/pathogen.json b/nextclade/resources/all/pathogen.json index b7ecb9fe..356c11db 100644 --- a/nextclade/resources/all/pathogen.json +++ b/nextclade/resources/all/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.01, "minLength": 1000 }, @@ -30,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -56,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/resources/all/reference.fasta b/nextclade/resources/all/reference.fasta index 1abd4ccc..08495c13 100644 --- a/nextclade/resources/all/reference.fasta +++ b/nextclade/resources/all/reference.fasta @@ -1,179 +1,2 @@ ->NC_002640.1 Dengue virus 4, complete genome -AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAG -TTCTAACAGTTTGTTTGAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGG -TGGTTAGACCACCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAG -GGTTGGTGAAGAGATTCTCAACCGGACTTTTTTCTGGGAAAGGACCCTTACGGATGGTGC -TAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAGA -GATGGGGACAGTTGAAGAAAAATAAGGCCATCAAGATACTGATTGGATTCAGGAAGGAGA -TAGGCCGCATGCTGAACATCTTGAACGGGAGAAAAAGGTCAACGATAACATTGCTGTGCT -TGATTCCCACCGTAATGGCGTTTTCCCTCAGCACAAGAGATGGCGAACCCCTCATGATAG -TGGCAAAACATGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAAT -GCACTCTCATTGCCATGGACTTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCC -CCCTACTGGTCAATACCGAACCTGAAGACATTGATTGCTGGTGCAACCTCACGTCTACCT -GGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAG -CTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGGATGTCATCGG -AAGGGGCTTGGAAGCATGCTCAGAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCG -CGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCT -TCTTTGTCCTAATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAA -ACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATG -GAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGA -CAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACA -TAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACC -AACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGT -TTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCA -ATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACA -CCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGT -CACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCA -GGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCG -TGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAG -AGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGAC -AGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCA -CAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTTAAGTGCAAAGTCC -GTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAA -TTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAG -GTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGG -TTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAG -AATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAA -CACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAG -GTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGAC -TGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGT -TTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCA -CGAACTCGAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGT -TTCTGGGCTTCACAGTTCAAGCAGACATGGGTTGTGTGGCGTCATGGAGTGGGAAAGAAT -TGAAGTGTGGAAGCGGAATTTTTGTGGTTGACAACGTGCACACTTGGACAGAACAGTACA -AATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCTGCAATATTAAATGCCCACAAAGATG -GGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAGCAAATAACCA -ACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTAGTGGCTGGGGATG -TGAAGGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCCCCAGTGAGTGATCTGAAAT -ATTCATGGAAGACATGGGGAAAAGCAAAAATCTTCACCCCAGAAGCAAGAAATAGCACAT -TTTTAATAGACGGACCAGACACCTCTGAATGCCCCAATGAACGAAGAGCATGGAACTCTC -TTGAGGTGGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTCCGAG -AAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCTGCAATTAAAGATCAGAAAG -CTGTGCATGCTGACATGGGTTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAG -AGAAAGCATCTCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACCCACACACTGTGGA -GCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAATCATATGCGGGCCCTTTTTCAC -AGCACAATTACCGCCAGGGCTATGCCACGCAAACCGTGGGCCCATGGCACTTAGGCAAAT -TAGAGATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACC -ATAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAACTAGTCACGCAATGGTGCT -GCCGCTCCTGCACGATGCCTCCCTTAAGGTTCTTGGGAGAAGATGGGTGCTGGTATGGGA -TGGAGATTAGGCCCTTGAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGACGGCCG -GACAGGGCACATCAGAAACTTTTTCTATGGGTCTGTTGTGCCTGACCTTGTTTGTGGAAG -AATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTAGTTGTGGTGATCACTCTTT -GTGCTATCATCCTGGGAGGCCTCACATGGATGGACTTACTACGAGCCCTCATCATGTTGG -GGGACACTATGTCTGGTAGAATAGGAGGACAGATCCACCTAGCCATCATGGCAGTGTTCA -AGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAG -CACTAATGGTAATAGGAATGGCCATGACAACGGTGCTTTCAATTCCACATGACCTTATGG -AACTCATTGATGGAATATCACTGGGACTAATTTTGCTAAAAATAGTAACACAGTTTGACA -ACACCCAAGTGGGAACCTTAGCTCTTTCCTTGACTTTCATAAGATCAACAATGCCATTGG -TCATGGCTTGGAGGACCATTATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTGTGCA -GGACAAGCTGTCTTCAAAAACAGTCTCATTGGGTAGAAATAACAGCACTCATCCTAGGAG -CCCAAGCTCTGCCAGTGTACCTAATGACTCTTATGAAAGGAGCCTCAAGAAGATCTTGGC -CTCTTAACGAGGGCATAATGGCTGTGGGTTTGGTTAGTCTCTTAGGAAGCGCTCTTTTAA -AGAATGATGTCCCTTTAGCTGGCCCAATGGTGGCAGGAGGCTTACTTCTGGCGGCTTACG -TGATGAGTGGTAGCTCAGCAGATCTGTCACTAGAGAAGGCCGCCAACGTGCAGTGGGATG -AAATGGCAGACATAACAGGCTCAAGCCCAATCGTAGAAGTGAAGCAGGATGAAGATGGCT -CTTTCTCCATACGGGACGTCGAGGAAACCAATATGATAACCCTTTTGGTGAAACTGGCAC -TGATAACAGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACCTTATGGTACA -TGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTCCCCTCACCCGCTGCCA -CTAAAAAAGCCGCACTGTCTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTATTCGGGA -AAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAA -CAAGAGGATCAGTGATCTGCCACGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCA -GGAATGACATGATATCATACGGTGGGGGATGGAGGCTTGGAGACAAATGGGACAAAGAAG -AAGACGTTCAGGTCCTCGCCATAGAACCAGGAAAAAATCCTAAACATGTCCAAACGAAAC -CTGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTAGATTTCAAACCCG -GAACGTCTGGTTCTCCCATCATCAACAGGAAAGGAAAAGTCATCGGACTCTATGGAAATG -GAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGAG -AGCCAGATTATGAAGTGGATGAGGACATTTTTCGAAAGAAAAGATTAACTATAATGGACT -TACACCCCGGAGCTGGAAAGACAAAAAGAATTCTTCCATCAATAGTGAGAGAAGCCTTAA -AAAGGAGGCTACGAACTTTGATTTTAGCTCCCACGAGAGTGGTGGCGGCCGAGATGGAAG -AGGCCCTACGTGGACTGCCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAG -GAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTTTTGTCATCAA -CCAGGGTTCCAAATTACAACCTTATAGTGATGGATGAAGCACATTTCACCGATCCTTCTA -GTGTCGCGGCTAGAGGATACATCTCGACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCT -TCATGACCGCAACCCCTCCCGGAGCGACAGATCCCTTTCCCCAGAGCAACAGCCCAATAG -AAGACATCGAGAGGGAAATTCCGGAAAGGTCATGGAACACAGGGTTCGACTGGATAACAG -ACTACCAAGGGAAAACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAA -ATTGTTTGAGAAAGTCGGGAAAGAAAGTTATCCAGTTGAGTAGGAAAACCTTTGATACAG -AGTATCCAAAAACGAAACTCACGGACTGGGACTTTGTGGTCACTACAGACATATCTGAAA -TGGGGGCCAATTTTAGAGCCGGGAGAGTGATAGACCCTAGAAGATGCCTCAAGCCAGTTA -TCCTACCAGATGGGCCAGAGAGAGTCATTTTAGCAGGTCCTATTCCAGTGACTCCAGCAA -GCGCTGCTCAGAGAAGAGGGCGAATAGGAAGGAACCCAGCACAAGAAGACGACCAATACG -TTTTCTCCGGAGACCCACTAAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGA -TGCTGCTTGACAATATCTACACCCCAGAAGGGATCATTCCAACATTGTTTGGTCCGGAAA -GGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTT -TTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCTG -CTGGCATTTCTTACGAAGATCGGGAATGGTGCTTCACAGGGGAAAGAAATAACCAAATTT -TAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAGCTAAGGC -CAAGATGGTTAGATGCACGTGTATACGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGT -TTGCCAGTGGAAGGAAGAGTATAACTCTCGACATCCTAACAGAGATTGCCAGTTTGCCAA -CTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGATAACATAGTCATGCTCCACACAACAG -AAAGAGGAGGGAGGGCCTATCAACACGCCCTGAACGAACTTCCGGAGTCACTGGAAACAC -TCATGCTTGTAGCTTTACTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTCATGCAAG -GGAAAGGAATAGGGAAATTGTCAATGGGTTTGATAACCATTGCGGTGGCTAGTGGCTTGC -TCTGGGTAGCAGAAATTCAACCCCAGTGGATAGCGGCCTCAATCATACTAGAGTTTTTTC -TCATGGTACTGTTGATACCGGAACCAGAAAAACAAAGGACCCCACAAGACAATCAATTGA -TCTACGTCATATTGACCATTCTCACCATCATTGGTCTAATAGCAGCCAACGAGATGGGGC -TGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCC -TCGATGTGGACTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACAATTC -TGACTCCCATGCTGAGACACACCATAGAAAACACGTCGGCCAACCTATCTCTAGCAGCCA -TTGCCAACCAGGCAGCCGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGG -ACCTCGGTGTGCCGCTGTTAGCAATGGGATGCTATTCTCAAGTGAACCCAACAACCTTGA -CAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGCCCAGGATTGCAGGCAA -AAGCCACAAGAGAGGCCCAGAAAAGGACAGCTGCTGGGATCATGAAAAATCCCACAGTGG -ACGGGATAACAGTAATAGATCTAGAACCAATATCCTATGACCCAAAATTTGAAAAGCAAT -TAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACAT -GGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAATCTTGACCTTGTGGGAGGGCA -ACCCGGGAAGGTTTTGGAACACGACCATAGCCGTATCCACCGCCAACATTTTCAGGGGAA -GTTACTTGGCGGGAGCTGGACTGGCTTTTTCACTCATAAAGAATGCACAAACCCCTAGGA -GGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCAT -TAGACAGAAAAGAGTTTGAAGAGTATAAAAGAAGTGGAATACTAGAAGTGGACAGGACTG -AAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTATCAAGAGGGTCCA -GTAAGATCAGATGGATTGTTGAGAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTAGATC -TTGGCTGTGGGAGAGGAGGATGGTCTTATTACATGGCGACACTCAAGAACGTGACTGAAG -TGAAAGGGTATACAAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACTTATG -GTTGGAATTTGGTCAAACTCCATTCAGGGGTTGACGTGTTCTACAAACCCACAGAGCAAG -TGGACACCCTGCTCTGTGATATTGGGGAGTCATCTTCTAATCCAACAATAGAGGAAGGAA -GAACATTAAGAGTTTTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCA -TCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAGCTGGAGAAACTGCAGAGAA -AACATGGTGGGAACCTTGTCAGATGCCCGCTGTCCAGGAACTCCACCCATGAGATGTATT -GGGTGTCAGGAGCGTCGGGAAACATTGTGAGCTCTGTGAACACAACATCAAAGATGTTGT -TGAACAGGTTCACAACAAGGCATAGGAAACCCACTTATGAGAAGGACGTAGATCTTGGGG -CAGGAACGAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAA -GGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACCTGGCATTATGATCAGGAAAACCCAT -ACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCTGCATCCTCCA -TGGTGAACGGGGTGGTAAAACTGCTAACAAAACCCTGGGATGTGATTCCAATGGTGACTC -AGTTAGCCATGACAGATACAACCCCTTTTGGGCAACAAAGAGTGTTCAAAGAGAAGGTGG -ATACCAGAACACCACAACCAAAACCCGGTACACGAATGGTTATGACCACGACAGCCAATT -GGCTGTGGGCCCTCCTTGGAAAGAAGAAAAATCCCAGACTGTGCACAAGGGAAGAGTTCA -TCTCAAAAGTTAGATCAAACGCAGCCATAGGCGCAGTCTTTCAGGAAGAACAGGGATGGA -CATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGG -CCCTACACCAGGAAGGGAAATGTGAATCGTGTGTCTATAACATGATGGGAAAACGTGAGA -AAAAGTTAGGAGAGTTTGGCAGAGCCAAGGGAAGCCGAGCAATCTGGTACATGTGGCTGG -GAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTTTTGAATGAAGATCACTGGTTTGGCA -GAGAAAATTCATGGAGTGGAGTGGAAGGGGAAGGTCTGCACAGATTGGGATATATCCTGG -AGGAGATAGACAAGAAGGATGGAGACCTAATGTATGCTGATGACACAGCAGGCTGGGACA -CAAGAATCACTGAGGATGACCTTCAAAATGAGGAACTGATCACGGAACAGATGGCTCCCC -ACCACAAGATCCTAGCCAAAGCCATTTTCAAACTAACCTATCAAAACAAAGTGGTGAAAG -TCCTCAGACCCACACCGCGGGGAGCGGTGATGGATATCATATCCAGGAAAGACCAAAGAG -GTAGTGGACAAGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTTCAACTCA -TCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGT -TGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTAAAGAGGATGG -CAATCAGTGGAGACGATTGCGTGGTGAAGCCCCTAGATGAGAGGTTTGGCACTTCCCTCC -TCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCTAAGG -GATGGAAAAACTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTTATGA -AGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCA -GAATCTCGCAGGGAGCTGGATGGAGCTTAAGAGAAACAGCCTGCCTGGGCAAAGCTTACG -CCCAGATGTGGTCGCTTATGTACTTCCACAGAAGGGATCTGCGTTTAGCCTCCATGGCCA -TATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACG -CTCATCACCAGTGGATGACCACTGAAGATATGCTCAAAGTGTGGAACAGAGTGTGGATAG -AAGACAACCCTAATATGACTGACAAGACTCCAGTCCATTCGTGGGAAGATATACCTTACC -TAGGGAAAAGAGAGGATTTGTGGTGTGGATCCCTGATTGGACTTTCTTCCAGAGCCACCT -GGGCGAAGAACATTCATACGGCCATAACCCAGGTCAGGAACCTGATCGGAAAAGAGGAAT -ACGTGGATTACATGCCAGTAATGAAAAGATACAGTGCTCCTTCAGAGAGTGAAGGAGTTC -TGTAATTACCAACAACAAACACCAAAGGCTATTGAAGTCAGGCCACTTGTGCCACGGTTT -GAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAATGGGAGGCGTAATAATCCCCAGGGAG -GCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCT -CCCATCACTGATAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTG -GTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGG -GAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGAT -GGATTGGTGTTGTTGATCCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome +AGTTGTTAGTCTACGTGGACCGACAAGGACAGTTTCGAATCGGAAGCTTGCTTAACGTAGTTCTAACAGTTTTTTTAATTAGAGAGCAGATCTCTGAGATGAACAACCAACGGAAAAAGGCGGGAAAACCGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCAACTGTACAACAGTTGGCGAAGAGATTCTCAATAGGATTGCTGTAAGGGCAAGGACCATTAAAATTGGTTATGGCTTTCATAGCATTCCTACGATTCCTAGCCATCCCACCAACAGCAGGGATTTTGAAAAGATGGGGAACATTCAAGAAGTCTAAGGCTATCAAGGTACTGAGAGGATTCAGGAAGGAGATCGGAAGCATGCTGAACATTTTGAACAGGAGAAAAAGAACAGCAATCATTCTCATGATGCTGATTCCAACAGTAATGGCGTTCCATTTGACCACACGAGATGGAGAGCCGCACATGATTGTGAGCAAGCATGAAAGAGGAAAATCCCTTCTGTTTAAGACAGCGGATGGAATCAACATGTGCACCCTCATTGCCATGGATCTGGGTGAGTTGTGTGAGGACACAATCACGTACAAATGCCCCCTTCTCACCGAAACCGAACCAGAAGACATTGACTGCTGGTGCAATCCCACGTCCACATGGGTGACCTATGGGACGTGTACCCAAACTGGAGAACACAGACGAGAGAAAAGATCAGTGGCACTAGCCCCACATGTGGGAATGGGACTGGAAACAAGAACTGAAACATGGATGTCATCAGAAGGAGCTTGGAAACAAGCCCAGAGAGTAGAGACTTGGATTCTGAGACACCCAGGATTCACGATAATGGCAGTATTTCTGGCATACACCATAGGAACAACATATATCCAGAGAGTCGTTATTTTTATCCTACTGATGCTGGTCGCCCCATCCATGACAATGCGATGCGTGGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTTTCAGGAGGAACGTGGGTTGACGTGGTGCTAGAACATGGAAGTTGTGTCACAACCATGGCAAAGAACAAACCAACACTGGACTTTGAACTGATGAAGACAGAAGCCAAACAACCGGCCACACTAAGGAAATTCTGCATTGAAGCTAAAATAACCAACACAACAACAGAATCAAGATGTCCAACACAAGGGGAACCCAATCTAGTAGAGGAGCAGGACCAGAAGTTCGTCTGCAAACAAACGATGGTGGACAGAGGATGGGGCAATGGCTGTGGTTTGTTTGGAAAAGGAGGCATTGTGACATGTGCGAAGTTTACATGCTTGAAGAAAATAGAAGGAAAAGTGGTGCAACCTGAAAACTTAGAATACACCGTGGTCATAACAGTCCACACAGGAGACGAACACGCAGTGGGAAATGACACAACAAAACATGGAATGACGGCCAAGATAACACCCCAGGCTTCCACCGCAGAAGCTAAACTGACAGACTATGGAACTCTCACGCTGGATTGCTCACCAAGAACAGGTCTCGACTTTAATGAGATGGTCTTGTTGAAAATGAAAAACAAAGCATGGCTTGTACACAGACAATGGTTCCTAGACCTACCTCTACCATGGACATCAGGAGCTGACACATAAGAAGCAAATTGGAACCAGAAAGAGATGCTGGTGACATTCAAAAATCCTCATGCAAAGAAACAGGATGTAGTCGTCCTAGGATCCCAAGAAGGAGCCATGCACACAGCACTCACAGGAGCTACAGAAATCCAAACGTCAGGAGGAAACTTAATGTTTGCAGGACACCTGAAGTGCAGACTGAGAATGGACAAACTGAAACTCAAAGGGATGTCATACGCGATGTGCACAGGAAAGTTCAAAATTGAGAAAGAAATGGCAGAAACACAGCATGGAACAATAGTCATTAAGGTTAAGTATGAAGGAGATGGTGCACCATGCAAGATCCCTTTTGAGATAAAGGATGTGAAAAAGAAAAATGTCATTGGGCGACTGATCACAGCCAACCCAATAGTCACAGAGAAAGACAGTCCAGTCAACATTGAAGCAGAACCTCCTTTTGGGGACAGCTACATCGTGATAGGAGTAGGAGAAAGAGCATTGAAACTCAACTGGTTCAAGAAAGGAAGCTCCATTGGGAAAATGTTTGAGGCAACTGCCAGAGGAGCAAAAAGAATGGCCATCTTGGGAGACACAGCCTGGGATTTTGGATCTGTAGGAGGAGTGTTCACATCAGTAGGAAAGGCGGTGCACCAGGTTTTTGGAACTGTCTATGGGGCTATGTTTAGCGGAGTCTCATGGACCATGAAAATCCTAATAGGGGTTCTCATAACATGGATAGGAATGAATTCAAGAAGCACTTCCCTGTCAATGACATGCATAGCAGTAGGAATCGTCACACTGTACCTGGGAGTCATGGTGCAGGCGGACATGGGTTGTGTTGTGAACTGGAAAGGCAAAGAACTGAAATGTGGAAGTGGAATTTTTGTCACTGACAACGTGCACACTTGGACAGAACAATACAAATTCCAACCAGACTCCCCAACAAGACTGGCGTCAGCCATTCCGAAAGCTCATGAGGAGGGAGTCTGTGGAATCCGATCAGCAACAAGACTGGAGAATCTCATGTGGAAGCAAATAACAAATGAATTGAACCACATCCTATGGGAAAATGAAATCAAACTAACTGTAGTGGCAGGAGACATTAAAGGAATCTTGGAGAAAGGGAAAAGAACACTTACACCTCAACCCATTGAGCTGAAATATTCATGGAAAACATGGGGAAAAGCAAAAATACTCACAGCAGAAGTACAAAATAACACCTTCCTCATAGACGGTCCAGACACACCAGAATGCCCTAATGACCAAAGAGCATGGAATTTTCTGGAAGTTGAGGACTATGGATTTGGAATCTTCACGACCAACATATGGCTGAAATTGCGAGAAGAGTACACCGAAGTGTGTGACCACAGGCTAATGTCAGCAGCCATCAAGGACAACAGGGCCGTCCATGCTGACATGGGCTATTGGATAGAAAGCGCAAAGAATGAGACCTGGAAGATAGAGAAAGCATCCTTCATTGAAGTTAAAACCTGCCTCTGGCCAAAATCACACACTCTTTGGAGCAATGGAGTGCTAGAAAGTGAAATGATAATTCCAAAGATTTTTGCTGGACCAATTTCACAGCACAACTACAGACCAGGCTATTACACACAAACAGCAGGACCATGGCACTTAGGCAAATTGGAGATGGACTTTGATTTTTGTGAAGGAACCACAGTTGTAGTGACTGAGGACTGTGGAAATAGAGGCCCATCTTTGAGAACAACCACAGCCTCAGGAAAACTGATAACTGAATGGTGCTGCCGATCTTGCACATTACCTCCCCTAAGATACATAGGAGAGGATGGATGCTGGTATGGGATGGAAATCAGACCCTTGAATGAGAAAGAAGAGAACCTGGTCAAGTCATTGGTCACAGCCGGGCATGGAAAGGTGGACAATTTTTCAATAGGACTCTTGTGCATGGCATTGTTCATGGAAGAGGTGCTGAGAACCAGAGTTGGCAGAAAACACATGATATTAGTAGTAGTGGTTACCTTCGTGACCCTCATCACAGGGAATATGACATGGAGAGACCTGGTAAGAGTACTTATCATGGTGGGAGCCACTATGTCTGATAGAATGGGGGGCGTGACTTACCTAGCTTTAATGGCAGCTTTCAAAATGAGACCAATCTTCGCAGTGGGATTGTTCTTGAGGAAACTGACTTCAAGAGAAATAATACTGATGACAATAGGAATGGCCCTGGTAACATCGTTCCAAATACCAGATGCCATTGTGGAACTGACTGATGGAATAGCATTGGGGATAATGGTGCTTAAAATGGTGACACATTTTGAAAAATACCAGTTGGGAGCGACCATCCTGTCCTTGACGTGCATCAAAACAACTATGACATTGCATAATGCATGGAAAACAATCACCATTATATTGGCAGTAGTTTCTCTTTTCCCATTGTGCCTGACTTCCTCCCTTCAAAAACAGACAGATTGGATACCAATAACATTGACAATCATAGGAGTCAAACCACTACCCATGTTTCTAATAACTTTAACAAAAACCAGCAAAAAAAGAAGTTGGCCTCTCAATGAGGGCATTATGGCTGTTGGAATGGTGAGCATTCTAGCAAGTTCTCTCCTAAAGAATGATGTTCCCATGGCTGGACCATTAGTGGCTGGAGGCTTGCTCATAGCGTGCTACGTGATAACTGGCAGCTCAGCAGACTTGTCACTGGAGAAAGCCGCCGATGTGAAATGGGAAGAAGAGGCAGAGATATCAGGAGCCAGCCCAATCATATTAGTCACAGTAGAAGAAGATGGTACCATGTCAATAAAGGATGAAGAGGAAGAGAACACACTAACCATACTCATAAAAACAGCACTGCTAGTAGTGTCAGGCCTCTTCCCATTGTCAATACCAGTCACAATGGCGGTATGGTACATGTGGCAAATGAAAAAACAAAGATCCGGAGTGCTGTGGGACGTCCCCTCACCCCCAGCAGTGGAAAAAGCTGAACTGGAAGATGGAGTCTATAGAATCAAGCAAAGAGGGATTTTTGGGAAATCCCAAGTTGGAGTTGGAGTATACAAAGAAGGAGTATTCCACACAATGTGGCACGTCACAAGAGGAGCTGTCCTCATGCATAAAGGGAAGAGACTGGAACCATCTTGGGCTGACGTCAAGAAAGACTTGATATCATATGGAGGAGGTTGGAGGCTTGAAGGAAAATGGAAAAAAGGAGAAGAAGTGCAGGTCTTGGCCGTAGAACCTGGGAAAAATCCAAAAAACGTCCAAACAAAACCTGGCCTTTTCAAGACCACTACAGGAGAAATAGGAGCCGTAGCCCTGGACTTCAAACCTGGAACATCAGGATCTCCCATCATTAACAAAAAAGGAAAAGTTGTGGGTCTCTATGGAAATGGAGTGGTTACAAAAAGTGGAGCCTATGTCAGTGCCATAGCGCAAACTGAAAAAATTGAAGAGCCGAATCCAGAGATTGAAGATGACATCTTTAGAAAGAAAAGATTAACCATAATGGACCTACATCCAGGAGCGGGAAAGACAAAAAGATATCTCCCAGCCATAGTCAGAGAGGCCATAAAAAGAAGCCTGAGAACTCTAATCTTGGCTCCCACAAGAGTGGTGGCAGCTGAAATGGAAGAAGCCCTAAGAGGACTCCCAATAAGTTATCAGACCCCAGCCATGAAGGCTGAACACACAGGAAGGGAGATTGTAGACCTAATGTGCCATGCCACTTTCACCATGAGACTGCTGTCACCAATCAGGGTTCCAAATTACAACCTGATAATAATGGATGAAGCACATTTCACAGACCCAGCCAGCATAGCGGCTAGAGGATACATCTCAACCCGAGTGGAAATGGGAGAGGCAGCTGCAATTTTTATGACAGCCACTCCCCCAGGAACGACAGATCCCTTTCCTCAGAGCAACGCCCCAATCAAAGATGAAGAAAGAGAAATTCCTGAACGCTCATGGAATTCAGGATATGAATGGATCACAGATTTTCAAGGGAAGACAGTGTGGTTTGTTCCAAGCATAAAAGCCGGAAATGACATAGCAAACTGCTTGAGAAAAAATGGAAAAAGGGTGATTCAACTGAGTAGGAAAACCTTTGACACAGAATATCCAAAAACAAAAATCAATGACTGGGACTTTGTGGTCACAACAGACATTTCCGAAATGGGAGCCAATTTCAAAGCTGAGAGAGTGATAGACCCAAGGAGATGCCTGAAGCCAGTTATACTGACAGATGGTCCAGAGCGGGTGATTCTGGCAGGACCCATGCCAGTGACCCTAGCAAGTGCTGCCCAAAGAAGAGGGAGAATAGGAAGGAACCCAAAAAAAGAAAATGACCAGTACATTTACATGGGAGAGCCTCTAAAAAATGATGAAGACCATGCTCACTGGACAGAAGCAAAGATGCTCCTTGACAACATCAACACACCAGAAGGGATCATCCCAACCCTGTTTGAACCAGAAAGGGAAAAGACTGAAGCCATAGACGGTGAATACCGCCTGAGAGGGGAAGCAAGGAAAACCTTTGTGGAACTAATGAGAAGAGGAGACCTACCAGTTTGGCTGGCCTACAAAGTAGCTTCAGAAGGCATCAAATACACAGACAGAAGGTGGTGCTTTGATGGAGAAAGGAACAATCAAATTTTGGAGGAGAACATGGAAGTGGAAATCTGGACAAAAGAAGGAGAAAGGAAGAAATTAAGACCTAGATGGTTGGATGCTAGAACTTATTCTGACCCACTGGCACTAAAGGAATTCAAGGAGTTTGCAGCTGGAAGAAAGTCCATAACCCTTGACCTAATAACAGAAATAGGTAGACTGCCAACTTACTTGACCCACAGGGCCAGAAATGCCCTGGACAACTTGGTCATGCTGCACACGACAGAAAAAGGAGGAAGGGCCTACAAACATGCTCTGAATGAACTACCAGAAACCCTGGAAACATTCATGCTCCTAGCTCTGTTGGCTGCGATGACAGGAGGAATCTTTCTGTTCTTGATGTAAGGAAGAGGTATAGGGAAAATGTCCATGGGACTGATCTGCATAATGGCAGCCAGCGGCCTGCTATGGATGGCAGAAATCCAGCCCCATTGGATAGCGGCCTCAATAATACTGGAGTTTTTTCTCATGGTACTGCTTATTCCAGAACCAGAAAAGCAGAGAACTCCCCAGGACAACCAATTGACCTATGTCGTGATAGCCATCCTCACAATGGTTGCAACAATAGCAGCCAATGAAATGGGATTGTTGGAAAAAACAAAGAAAGATCTTGGGTTTGGCCATGTAGCAACTGAAAATACAATTCTGGACGTAGATCTACGTCCAGCATCAGCATGGACACTCTATGCAGTGGCCACAACAATTATCACACCAATGTTGAGACACACCATAGAAAACTCCTCAGCAAATGTGTCCCTGACAGCCATTGCCAACCAGGCAGCGGTCTTGATGGGTCTTGGAAAAGGATGGCCATTATCGAAAATGGACATAGGAGTTCCACTTCTCGCCTTGGGATGCTATTCACAAGTGAACCCAATAACTCTCACAGCAGCACTACTTTTGCTAGTGGCACATTATGCCATAATAGGTCCAGGACTGCAAGCAAAAGCCACTAGAGAAGCTCAGAAAAGGACAGCAGCTGGAATCATGAAGAATCCAACGGTGGATGGGATAACAGTAATAGACCTAGATCCAATACCCTATGATCCAAAATTTGAAAAGCAGTTAGGACAAGTAATGCTCCTGGTCCTTTGTGCAGCACAGCTACTGTTGATGAGAACTACATGGGCTTTGTGTGAAGCCTTAACCCTAGCCACAGGACCAATATCAACACTGTGGGAAGGAAATCCAGGGAAATTCTGGAACACAACGATAGCTGTGTCCATGGCTAACATTTTCAGAGGGAGTTATTTGGCCGGAGCTGGACTTGCTTTTTCTATCATGAAGAATGCAGGAAGCGCAAGGAGAGGAACTGGGACCATAGGAGAAACACTGGGAGAAAAATGGAAAAGACAACTAAACCCATTGGGCAGGAAAGAATTCGAAATATACAAGAAAAGTGGAATTCTAGAAGTGGACAGAACCGAAGCCAAAGAAGGCTTGAAAAGAGGAGAAACAACCCACCATGCCGTGTCGAGAGGCTCCGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCAAACCAGAAGGGAAAGTCGTAGACCTTGGTTGTGGAAGAGGAGGCTGGTCATATTACTGTGCGGGACTGAAGAATGTGACAGAAGTGAAAGGATACACAAAAGGAGGACCAGGACATGAAGAACCAATCCCTATGTCTACATATGGATGGAACCTAGTCAAGCTTCAGAGTGGAGTGGATGTGTTCTTCACTCCACCTGAGAAATGTGACACCCTGTTGTGTGACATTGGGGAATCATCACCAAATCCAACAGTAGAAGAAGGAAGAACATTAAGAGTTCTGAAGATGGTGGAACCATGGCTCAACAACAACACTCAATTTTGCATAAAAGTTCTCAACCCCTACATGCCAACAGTCATAGAAAAACTGGAAAAACTACAAAGGAAACATGGAGGAATCCTTGTGAGAAATCCACTCTCACGAAATTCCACCCATGAGATGTACTGGGTGTCCAATGCTTCAGGAAACATTGTGTCTTCAGTGAACATGATATCAAGAATGTTGCTGAACAGATTCACAATGAGACACAGGAAACCCACTTATGAGAAAGACGTGGACCTTGGAGCTGGAACACGAAATGTCGCAATTGAAACAGAAACACCAAACATGGATATCATTGGGAAAAGGATAGAGAAAATAAAAGAAGAGCATAAAACAACATGGCACTATGATCAGGACAATCCATACAAAACATGGGCTTACCATGGAAGCTATGAAGCCAAACCGACAGGATCAGCATCATCCATGGTGAATGGAGTGGTGAGACTGCTGACAAAACCCTGGGACGTGATTCCCATGGTGACACAGATGGCAATGACAGACACAACTCCCTTTGGACAACAGAGAGTTTTTAAAGAGAAAGTGGACACGAGAACACCAAAACCAAAACCAGGCACAAGAAAAGTTATGAAGATCACAGCCGAGTGGCTTTGGAGATTCCTTGGAAGGAAAAAAAAACCCAGAATGTGCACAAGAGAAGAGTTCACAAAAAAAGTTAGAACCAACGCAGCTATGGGCGCCGTGTTCACTGATGAGAACAAATGGAACTCAGCAAGTGAAGCTGTTGAAGACGAACGGTTTTGGGAACTGGTGGACAAAGAAAGGGATCTTCACCAAGAAGGAAAGTGTGAAACGTGTGTCTACAACATGATGGGAAAAAGAGAGAAGAAACTAGGAGAGTTTGGCAAAGCAAAAGGCAGCAGAGCAATATGGTACATGTGGCTGGGAGCACGCTTCCTAGAGTTTGAAGCCCTAGGTTTCTTGAATGAAGACCACTGGTTCTCCAGAGAAAATTCACTGAGTGGAGTGGAAGGAGAAGGACTGCACAAGCTGGGATACATCCTAAGAGACATAAACAAGAAAGAAGGAGGAGCAATGTATGCTGATGACACAGCTGGTTGGGACACAAGAATCACAGAAGATGACCTGCAGAATGAAGAAATGATCACAGACCAAATGGACCCTGAACATAAGAAATTGGCCAAGGCCATTTTCAAACTAACATACCAAAACAAGGTGGTGAGAGTCCAAAGACCAACACCAAAAGGCACGGTGATGGATATCATATCCAGGAGAGACCAAAGAGGCAGTGGACAGGTTGGAACTTATGGTCTGAACACTTTCACCAACATGGAAGCACAACTAATCAGACAAATGGAAGGTGAAGGAGTCTTTACACCAAAAGAATTCTAGACCCCACATCTGCTAGAAAAAAGAGTTCAAGAATGGTTGGAAAAACATGGAGTCGAAAGGTTAAAAAGAATGGCAATCAGTGGAGATGATTGTGTGGTGAAACCACTAGATGACAGGTTCGCCACAGCCCTAACAGCTTTGAATGACATGGGAAAGGTTAGGAAAGACATACCGCAATGGGAACCTTCAAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGCTCCCACCACTTTCATGAGCTGATCATGAAAGATGGTCGCACGCTAGTAGTTCCATGCAGAAACCAAGATGAACTGATAGGTAGAGCCAGAATCTCTCAGGGAGCTGGATGGAGCTTGAGAGAAACAGCCTGTCTGGGGAAGTCTTACGCCCAAATGTGGAGGCTGATGTACTTCCACAGAAGAGATCTGAGGCTGGCGGCCAATGCCATATGTTCAGCAGTTCCAGTACATTGGGTTCCAACAAGCAGAACAACCTGGTCGATCCATGCCCACCATCAATGGATGACAACAGAAGACATGTTTACAGTCTGGAACAGGGTGTGGATAGAGGACAACCCATGGATGGAAGACAAAACTCCAGTCTAATCTTGGGAAGACATACCATACCTAGGGAAAAGAGAAGACCAGTGGTGTGGATCCCTGATTGGCCTAACATCCAGGGCCACCTGGGCAAAGAACATTCAAACAGCCATAAACCAAGTCAGAAGCCTCATTGGGAATGAGGAGTATATAGATTACATGCCATCAATGAAAAGATTCAGGAATGAGGAGGAGAACGAAGGAGTTCTGTGGTAAACAGCAAAAGAAGTCAGGCATAAAAGAAGTCAGGCCACTAATGCCACGGCTTGAGCAAACCGTGCTGCCTGTAGCTCCACCAAAAAGGGGAGGTGTAAAAAAACCCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGTGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCATGACAGACAAAACGCAGCACAAGGGGGCCCAAAGCCAGGAGGAAGCTGTACTCTCGTTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAAAACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/resources/denv1/genome_annotation.gff3 b/nextclade/resources/denv1/genome_annotation.gff3 index 14201ebb..aa3a8428 100644 --- a/nextclade/resources/denv1/genome_annotation.gff3 +++ b/nextclade/resources/denv1/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_001477.1 1 10735 -NC_001477.1 feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; -NC_001477.1 feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; -NC_001477.1 feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; -NC_001477.1 feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; -NC_001477.1 feature gene 2420 3475 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_001477.1 feature gene 3476 4129 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_001477.1 feature gene 4130 4519 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_001477.1 feature gene 4520 6376 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_001477.1 feature gene 6377 6757 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_001477.1 feature gene 6758 6826 . + . codon_start=1;gene=2K;gene_name=2K; -NC_001477.1 feature gene 6827 7573 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_001477.1 feature gene 7574 10270 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome 1 10735 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 2420 3475 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 3476 4129 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 4130 4519 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 4520 6376 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 6377 6757 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 6758 6826 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 6827 7573 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome feature gene 7574 10270 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/resources/denv1/pathogen.json b/nextclade/resources/denv1/pathogen.json index 5ebe4c90..52d9ee02 100644 --- a/nextclade/resources/denv1/pathogen.json +++ b/nextclade/resources/denv1/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/resources/denv1/reference.fasta b/nextclade/resources/denv1/reference.fasta index 3a18135a..061492e4 100644 --- a/nextclade/resources/denv1/reference.fasta +++ b/nextclade/resources/denv1/reference.fasta @@ -1,180 +1,2 @@ ->NC_001477.1 Dengue virus 1, complete genome -AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGAATCGGAAGCTTGCTTAACGTAG -TTCTAACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGG -TCGACCGTCTTTCAATATGCTGAAACGCGCGAGAAACCGCGTGTCAACTGTTTCACAGTT -GGCGAAGAGATTCTCAAAAGGATTGCTTTCAGGCCAAGGACCCATGAAATTGGTGATGGC -TTTTATAGCATTCCTAAGATTTCTAGCCATACCTCCAACAGCAGGAATTTTGGCTAGATG -GGGCTCATTCAAGAAGAATGGAGCGATCAAAGTGTTACGGGGTTTCAAGAAAGAAATCTC -AAACATGTTGAACATAATGAACAGGAGGAAAAGATCTGTGACCATGCTCCTCATGCTGCT -GCCCACAGCCCTGGCGTTCCATCTGACCACCCGAGGGGGAGAGCCGCACATGATAGTTAG -CAAGCAGGAAAGAGGAAAATCACTTTTGTTTAAGACCTCTGCAGGTGTCAACATGTGCAC -CCTTATTGCAATGGATTTGGGAGAGTTATGTGAGGACACAATGACCTACAAATGCCCCCG -GATCACTGAGACGGAACCAGATGACGTTGACTGTTGGTGCAATGCCACGGAGACATGGGT -GACCTATGGAACATGTTCTCAAACTGGTGAACACCGACGAGACAAACGTTCCGTCGCACT -GGCACCACACGTAGGGCTTGGTCTAGAAACAAGAACCGAAACGTGGATGTCCTCTGAAGG -CGCTTGGAAACAAATACAAAAAGTGGAGACCTGGGCTCTGAGACACCCAGGATTCACGGT -GATAGCCCTTTTTCTAGCACATGCCATAGGAACATCCATCACCCAGAAAGGGATCATTTT -TATTTTGCTGATGCTGGTAACTCCATCCATGGCCATGCGGTGCGTGGGAATAGGCAACAG -AGACTTCGTGGAAGGACTGTCAGGAGCTACGTGGGTGGATGTGGTACTGGAGCATGGAAG -TTGCGTCACTACCATGGCAAAAGACAAACCAACACTGGACATTGAACTCTTGAAGACGGA -GGTCACAAACCCTGCCGTCCTGCGCAAACTGTGCATTGAAGCTAAAATATCAAACACCAC -CACCGATTCGAGATGTCCAACACAAGGAGAAGCCACGCTGGTGGAAGAACAGGACACGAA -CTTTGTGTGTCGACGAACGTTCGTGGACAGAGGCTGGGGCAATGGTTGTGGGCTATTCGG -AAAAGGTAGCTTAATAACGTGTGCTAAGTTTAAGTGTGTGACAAAACTGGAAGGAAAGAT -AGTCCAATATGAAAACTTAAAATATTCAGTGATAGTCACCGTACACACTGGAGACCAGCA -CCAAGTTGGAAATGAGACCACAGAACATGGAACAACTGCAACCATAACACCTCAAGCTCC -CACGTCGGAAATACAGCTGACAGACTACGGAGCTCTAACATTGGATTGTTCACCTAGAAC -AGGGCTAGACTTTAATGAGATGGTGTTGTTGACAATGAAAAAAAAATCATGGCTCGTCCA -CAAACAATGGTTTCTAGACTTACCACTGCCTTGGACCTCGGGGGCTTCAACATCCCAAGA -GACTTGGAATAGACAAGACTTGCTGGTCACATTTAAGACAGCTCATGCAAAAAAGCAGGA -AGTAGTCGTACTAGGATCACAAGAAGGAGCAATGCACACTGCGTTGACTGGAGCGACAGA -AATCCAAACGTCTGGAACGACAACAATTTTTGCAGGACACCTGAAATGCAGATTAAAAAT -GGATAAACTGATTTTAAAAGGGATGTCATATGTAATGTGCACAGGGTCATTCAAGTTAGA -GAAGGAAGTGGCTGAGACCCAGCATGGAACTGTTCTAGTGCAGGTTAAATACGAAGGAAC -AGATGCACCATGCAAGATCCCCTTCTCGTCCCAAGATGAGAAGGGAGTAACCCAGAATGG -GAGATTGATAACAGCCAACCCCATAGTCACTGACAAAGAAAAACCAGTCAACATTGAAGC -GGAGCCACCTTTTGGTGAGAGCTACATTGTGGTAGGAGCAGGTGAAAAAGCTTTGAAACT -AAGCTGGTTCAAGAAGGGAAGCAGTATAGGGAAAATGTTTGAAGCAACTGCCCGTGGAGC -ACGAAGGATGGCCATCCTGGGAGACACTGCATGGGACTTCGGTTCTATAGGAGGGGTGTT -CACGTCTGTGGGAAAACTGATACACCAGATTTTTGGGACTGCGTATGGAGTTTTGTTCAG -CGGTGTTTCTTGGACCATGAAGATAGGAATAGGGATTCTGCTGACATGGCTAGGATTAAA -CTCAAGGAGCACGTCCCTTTCAATGACGTGTATCGCAGTTGGCATGGTCACACTGTACCT -AGGAGTCATGGTTCAGGCGGACTCGGGATGTGTAATCAACTGGAAAGGCAGAGAACTCAA -ATGTGGAAGCGGCATTTTTGTCACCAATGAAGTCCACACCTGGACAGAGCAATATAAATT -CCAGGCCGACTCCCCTAAGAGACTATCAGCGGCCATTGGGAAGGCATGGGAGGAGGGTGT -GTGTGGAATTCGATCAGCCACTCGTCTCGAGAACATCATGTGGAAGCAAATATCAAATGA -ATTAAACCACATCTTACTTGAAAATGACATGAAATTTACAGTGGTCGTAGGAGACGTTAG -TGGAATCTTGGCCCAAGGAAAGAAAATGATTAGGCCACAACCCATGGAACACAAATACTC -GTGGAAAAGCTGGGGAAAAGCCAAAATCATAGGAGCAGATGTACAGAATACCACCTTCAT -CATCGACGGCCCAAACACCCCAGAATGCCCTGATAACCAAAGAGCATGGAACATTTGGGA -AGTTGAAGACTATGGATTTGGAATTTTCACGACAAACATATGGTTGAAATTGCGTGACTC -CTACACTCAAGTGTGTGACCACCGGCTAATGTCAGCTGCCATCAAGGATAGCAAAGCAGT -CCATGCTGACATGGGGTACTGGATAGAAAGTGAAAAGAACGAGACTTGGAAGTTGGCAAG -AGCCTCCTTCATAGAAGTTAAGACATGCATCTGGCCAAAATCCCACACTCTATGGAGCAA -TGGAGTCCTGGAAAGTGAGATGATAATCCCAAAGATATATGGAGGACCAATATCTCAGCA -CAACTACAGACCAGGATATTTCACACAAACAGCAGGGCCGTGGCACTTGGGCAAGTTAGA -ACTAGATTTTGATTTATGTGAAGGTACCACTGTTGTTGTGGATGAACATTGTGGAAATCG -AGGACCATCTCTTAGAACCACAACAGTCACAGGAAAGACAATCCATGAATGGTGCTGTAG -ATCTTGCACGTTACCCCCCCTACGTTTCAAAGGAGAAGACGGGTGCTGGTACGGCATGGA -AATCAGACCAGTCAAGGAGAAGGAAGAGAACCTAGTTAAGTCAATGGTCTCTGCAGGGTC -AGGAGAAGTGGACAGTTTTTCACTAGGACTGCTATGCATATCAATAATGATCGAAGAGGT -AATGAGATCCAGATGGAGCAGAAAAATGCTGATGACTGGAACATTGGCTGTGTTCCTCCT -TCTCACAATGGGACAATTGACATGGAATGATCTGATCAGGCTATGTATCATGGTTGGAGC -CAACGCTTCAGACAAGATGGGGATGGGAACAACGTACCTAGCTTTGATGGCCACTTTCAG -AATGAGACCAATGTTCGCAGTCGGGCTACTGTTTCGCAGATTAACATCTAGAGAAGTTCT -TCTTCTTACAGTTGGATTGAGTCTGGTGGCATCTGTAGAACTACCAAATTCCTTAGAGGA -GCTAGGGGATGGACTTGCAATGGGCATCATGATGTTGAAATTACTGACTGATTTTCAGTC -ACATCAGCTATGGGCTACCTTGCTGTCTTTAACATTTGTCAAAACAACTTTTTCATTGCA -CTATGCATGGAAGACAATGGCTATGATACTGTCAATTGTATCTCTCTTCCCTTTATGCCT -GTCCACGACTTCTCAAAAAACAACATGGCTTCCGGTGTTGCTGGGATCTCTTGGATGCAA -ACCACTAACCATGTTTCTTATAACAGAAAACAAAATCTGGGGAAGGAAAAGCTGGCCTCT -CAATGAAGGAATTATGGCTGTTGGAATAGTTAGCATTCTTCTAAGTTCACTTCTCAAGAA -TGATGTGCCACTAGCTGGCCCACTAATAGCTGGAGGCATGCTAATAGCATGTTATGTCAT -ATCTGGAAGCTCGGCCGATTTATCACTGGAGAAAGCGGCTGAGGTCTCCTGGGAAGAAGA -AGCAGAACACTCTGGTGCCTCACACAACATACTAGTGGAGGTCCAAGATGATGGAACCAT -GAAGATAAAGGATGAAGAGAGAGATGACACACTCACCATTCTCCTCAAAGCAACTCTGCT -AGCAATCTCAGGGGTATACCCAATGTCAATACCGGCGACCCTCTTTGTGTGGTATTTTTG -GCAGAAAAAGAAACAGAGATCAGGAGTGCTATGGGACACACCCAGCCCTCCAGAAGTGGA -AAGAGCAGTCCTTGATGATGGCATTTATAGAATTCTCCAAAGAGGATTGTTGGGCAGGTC -TCAAGTAGGAGTAGGAGTTTTTCAAGAAGGCGTGTTCCACACAATGTGGCACGTCACCAG -GGGAGCTGTCCTCATGTACCAAGGGAAGAGACTGGAACCAAGTTGGGCCAGTGTCAAAAA -AGACTTGATCTCATATGGAGGAGGTTGGAGGTTTCAAGGATCCTGGAACGCGGGAGAAGA -AGTGCAGGTGATTGCTGTTGAACCGGGGAAGAACCCCAAAAATGTACAGACAGCGCCGGG -TACCTTCAAGACCCCTGAAGGCGAAGTTGGAGCCATAGCTCTAGACTTTAAACCCGGCAC -ATCTGGATCTCCTATCGTGAACAGAGAGGGAAAAATAGTAGGTCTTTATGGAAATGGAGT -GGTGACAACAAGTGGTACCTACGTCAGTGCCATAGCTCAAGCTAAAGCATCACAAGAAGG -GCCTCTACCAGAGATTGAGGACGAGGTGTTTAGGAAAAGAAACTTAACAATAATGGACCT -ACATCCAGGATCGGGAAAAACAAGAAGATACCTTCCAGCCATAGTCCGTGAGGCCATAAA -AAGAAAGCTGCGCACGCTAGTCTTAGCTCCCACAAGAGTTGTCGCTTCTGAAATGGCAGA -GGCGCTCAAGGGAATGCCAATAAGGTATCAGACAACAGCAGTGAAGAGTGAACACACGGG -AAAGGAGATAGTTGACCTTATGTGTCACGCCACTTTCACTATGCGTCTCCTGTCTCCTGT -GAGAGTTCCCAATTATAATATGATTATCATGGATGAAGCACATTTTACCGATCCAGCCAG -CATAGCAGCCAGAGGGTATATCTCAACCCGAGTGGGTATGGGTGAAGCAGCTGCGATTTT -CATGACAGCCACTCCCCCCGGATCGGTGGAGGCCTTTCCACAGAGCAATGCAGTTATCCA -AGATGAGGAAAGAGACATTCCTGAAAGATCATGGAACTCAGGCTATGACTGGATCACTGA -TTTCCCAGGTAAAACAGTCTGGTTTGTTCCAAGCATCAAATCAGGAAATGACATTGCCAA -CTGTTTAAGAAAGAATGGGAAACGGGTGGTCCAATTGAGCAGAAAAACTTTTGACACTGA -GTACCAGAAAACAAAAAATAACGACTGGGACTATGTTGTCACAACAGACATATCCGAAAT -GGGAGCAAACTTCCGAGCCGACAGGGTAATAGACCCGAGGCGGTGCCTGAAACCGGTAAT -ACTAAAAGATGGCCCAGAGCGTGTCATTCTAGCCGGACCGATGCCAGTGACTGTGGCTAG -CGCCGCCCAGAGGAGAGGAAGAATTGGAAGGAACCAAAATAAGGAAGGCGATCAGTATAT -TTACATGGGACAGCCTCTAAACAATGATGAGGACCACGCCCATTGGACAGAAGCAAAAAT -GCTCCTTGACAACATAAACACACCAGAAGGGATTATCCCAGCCCTCTTTGAGCCGGAGAG -AGAAAAGAGTGCAGCAATAGACGGGGAATACAGACTACGGGGTGAAGCGAGGAAAACGTT -CGTGGAGCTCATGAGAAGAGGAGATCTACCTGTCTGGCTATCCTACAAAGTTGCCTCAGA -AGGCTTCCAGTACTCCGACAGAAGGTGGTGCTTTGATGGGGAAAGGAACAACCAGGTGTT -GGAGGAGAACATGGACGTGGAGATCTGGACAAAAGAAGGAGAAAGAAAGAAACTACGACC -CCGCTGGCTGGATGCCAGAACATACTCTGACCCACTGGCTCTGCGCGAATTCAAAGAGTT -CGCAGCAGGAAGAAGAAGCGTCTCAGGTGACCTAATATTAGAAATAGGGAAACTTCCACA -ACATTTAACGCAAAGGGCCCAGAACGCCTTGGACAATCTGGTTATGTTGCACAACTCTGA -ACAAGGAGGAAAAGCCTATAGACACGCCATGGAAGAACTACCAGACACCATAGAAACGTT -AATGCTCCTAGCTTTGATAGCTGTGCTGACTGGTGGAGTGACGTTGTTCTTCCTATCAGG -AAGGGGTCTAGGAAAAACATCCATTGGCCTACTCTGCGTGATTGCCTCAAGTGCACTGTT -ATGGATGGCCAGTGTGGAACCCCATTGGATAGCGGCCTCTATCATACTGGAGTTCTTTCT -GATGGTGTTGCTTATTCCAGAGCCGGACAGACAGCGCACTCCACAAGACAACCAGCTAGC -ATACGTGGTGATAGGTCTGTTATTCATGATATTGACAGTGGCAGCCAATGAGATGGGATT -ACTGGAAACCACAAAGAAGGACCTGGGGATTGGTCATGCAGCTGCTGAAAACCACCATCA -TGCTGCAATGCTGGACGTAGACCTACATCCAGCTTCAGCCTGGACTCTCTATGCAGTGGC -CACAACAATTATCACTCCCATGATGAGACACACAATTGAAAACACAACGGCAAATATTTC -CCTGACAGCTATTGCAAACCAGGCAGCTATATTGATGGGACTTGACAAGGGATGGCCAAT -ATCAAAGATGGACATAGGAGTTCCACTTCTCGCCTTGGGGTGCTATTCTCAGGTGAACCC -GCTGACGCTGACAGCGGCGGTATTGATGCTAGTGGCTCATTATGCCATAATTGGACCCGG -ACTGCAAGCAAAAGCTACTAGAGAAGCTCAAAAAAGGACAGCAGCCGGAATAATGAAAAA -CCCAACTGTCGACGGGATCGTTGCAATAGATTTGGACCCTGTGGTTTACGATGCAAAATT -TGAAAAACAGCTAGGCCAAATAATGTTGTTGATACTTTGCACATCACAGATCCTCCTGAT -GCGGACCACATGGGCCTTGTGTGAATCCATCACACTAGCCACTGGACCTCTGACTACGCT -TTGGGAGGGATCTCCAGGAAAATTCTGGAACACCACGATAGCGGTGTCCATGGCAAACAT -TTTTAGGGGAAGTTATCTAGCAGGAGCAGGTCTGGCCTTTTCATTAATGAAATCTCTAGG -AGGAGGTAGGAGAGGCACGGGAGCCCAAGGGGAAACACTGGGAGAAAAATGGAAAAGACA -GCTAAACCAATTGAGCAAGTCAGAATTCAACACTTACAAAAGGAGTGGGATTATAGAGGT -GGATAGATCTGAAGCCAAAGAGGGGTTAAAAAGAGGAGAAACGACTAAACACGCAGTGTC -GAGAGGAACGGCCAAACTGAGGTGGTTTGTGGAGAGGAACCTTGTGAAACCAGAAGGGAA -AGTCATAGACCTCGGTTGTGGAAGAGGTGGCTGGTCATATTATTGCGCTGGGCTGAAGAA -AGTCACAGAAGTGAAAGGATACACGAAAGGAGGACCTGGACATGAGGAACCAATCCCAAT -GGCAACCTATGGATGGAACCTAGTAAAGCTATACTCCGGGAAAGATGTATTCTTTACACC -ACCTGAGAAATGTGACACCCTCTTGTGTGATATTGGTGAGTCCTCTCCGAACCCAACTAT -AGAAGAAGGAAGAACGTTACGTGTTCTAAAGATGGTGGAACCATGGCTCAGAGGAAACCA -ATTTTGCATAAAAATTCTAAATCCCTATATGCCGAGTGTGGTAGAAACTTTGGAGCAAAT -GCAAAGAAAACATGGAGGAATGCTAGTGCGAAATCCACTCTCAAGAAACTCCACTCATGA -AATGTACTGGGTTTCATGTGGAACAGGAAACATTGTGTCAGCAGTAAACATGACATCTAG -AATGCTGCTAAATCGATTCACAATGGCTCACAGGAAGCCAACATATGAAAGAGACGTGGA -CTTAGGCGCTGGAACAAGACATGTGGCAGTAGAACCAGAGGTGGCCAACCTAGATATCAT -TGGCCAGAGGATAGAGAATATAAAAAATGAACACAAATCAACATGGCATTATGATGAGGA -CAATCCATACAAAACATGGGCCTATCATGGATCATATGAGGTCAAGCCATCAGGATCAGC -CTCATCCATGGTCAATGGTGTGGTGAGACTGCTAACCAAACCATGGGATGTCATTCCCAT -GGTCACACAAATAGCCATGACTGACACCACACCCTTTGGACAACAGAGGGTGTTTAAAGA -GAAAGTTGACACGCGTACACCAAAAGCGAAACGAGGCACAGCACAAATTATGGAGGTGAC -AGCCAGGTGGTTATGGGGTTTTCTCTCTAGAAACAAAAAACCCAGAATCTGCACAAGAGA -GGAGTTCACAAGAAAAGTCAGGTCAAACGCAGCTATTGGAGCAGTGTTCGTTGATGAAAA -TCAATGGAACTCAGCAAAAGAGGCAGTGGAAGATGAACGGTTCTGGGACCTTGTGCACAG -AGAGAGGGAGCTTCATAAACAAGGAAAATGTGCCACGTGTGTCTACAACATGATGGGAAA -GAGAGAGAAAAAATTAGGAGAGTTCGGAAAGGCAAAAGGAAGTCGCGCAATATGGTACAT -GTGGTTGGGAGCGCGCTTTTTAGAGTTTGAAGCCCTTGGTTTCATGAATGAAGATCACTG -GTTCAGCAGAGAGAATTCACTCAGTGGAGTGGAAGGAGAAGGACTCCACAAACTTGGATA -CATACTCAGAGACATATCAAAGATTCCAGGGGGAAATATGTATGCAGATGACACAGCCGG -ATGGGACACAAGAATAACAGAGGATGATCTTCAGAATGAGGCCAAAATCACTGACATCAT -GGAACCTGAACATGCCCTATTGGCCACGTCAATCTTTAAGCTAACCTACCAAAACAAGGT -AGTAAGGGTGCAGAGACCAGCGAAAAATGGAACCGTGATGGATGTCATATCCAGACGTGA -CCAGAGAGGAAGTGGACAGGTTGGAACCTATGGCTTAAACACCTTCACCAACATGGAGGC -CCAACTAATAAGACAAATGGAGTCTGAGGGAATCTTTTCACCCAGCGAATTGGAAACCCC -AAATCTAGCCGAAAGAGTCCTCGACTGGTTGAAAAAACATGGCACCGAGAGGCTGAAAAG -AATGGCAATCAGTGGAGATGACTGTGTGGTGAAACCAATCGATGACAGATTTGCAACAGC -CTTAACAGCTTTGAATGACATGGGAAAGGTAAGAAAAGACATACCGCAATGGGAACCTTC -AAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGTTCACACCATTTCCACCAGCTGAT -TATGAAGGATGGGAGGGAGATAGTGGTGCCATGCCGCAACCAAGATGAACTTGTAGGTAG -GGCCAGAGTATCACAAGGCGCCGGATGGAGCTTGAGAGAAACTGCATGCCTAGGCAAGTC -ATATGCACAAATGTGGCAGCTGATGTACTTCCACAGGAGAGACTTGAGATTAGCGGCTAA -TGCTATCTGTTCAGCCGTTCCAGTTGATTGGGTCCCAACCAGCCGCACCACCTGGTCGAT -CCATGCCCACCATCAATGGATGACAACAGAAGACATGTTGTCAGTGTGGAATAGGGTTTG -GATAGAGGAAAACCCATGGATGGAGGACAAGACTCATGTGTCCAGTTGGGAAGACGTTCC -ATACCTAGGAAAAAGGGAAGATCAATGGTGTGGTTCCCTAATAGGCTTAACAGCACGAGC -CACCTGGGCCACCAACATACAAGTGGCCATAAACCAAGTGAGAAGGCTCATTGGGAATGA -GAATTATCTAGACTTCATGACATCAATGAAGAGATTCAAAAACGAGAGTGATCCCGAAGG -GGCACTCTGGTAAGCCAACTCATTCACAAAATAAAGGAAAATAAAAAATCAAACAAGGCA -AGAAGTCAGGCCGGATTAAGCCATAGCACGGTAAGAGCTATGCTGCCTGTGAGCCCCGTC -CAAGGACGTAAAATGAAGTCAGGCCGAAAGCCACGGTTCGAGCAAGCCGTGCTGCCTGTA -GCTCCATCGTGGGGATGTAAAAACCCGGGAGGCTGCAAACCATGGAAGCTGTACGCATGG -GGTAGCAGACTAGTGGTTAGAGGAGACCCCTCCCAAGACACAACGCAGCAGCGGGGCCCA -ACACCAGGGGAAGCTGTACCCTGGTGGTAAGGACTAGAGGTTAGAGGAGACCCCCCGCAC -AACAACAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCTACAGCATC -ATTCCAGGCACAGAACGCCAAAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome +AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGAATCGGAAGCTTGCTTAACGTAGTTCTAACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGTCGACCGTCTTTCAATATGCTGAAACGCGCGAGAAACCGCGTGTCAACTGTTTCACAGTTGGCGAAGAGATTCTCAAAAGGATTGCTCTCAGGCCAAGGACCCATGAAATTGGTGATGGCTTTCATAGCATTCCTAAGATTTCTAGCCATACCCCCAACAGCAGGAATTTTGGCTAGATGGGGCTCATTCAAGAAGAATGGAGCGATTAAAGTGTTACGGGGTTTCAAGAAAGAAATCTCAAACATGTTGAACATAATGAACAGGAGGAAAAGATCCGTGACCATGCTCCTTATGCTGCTGCCCACAGCCCTGGCGTTCCATCTGACCACACGAGGGGGAGAGCCGCACATGATAGTTAGCAAGCAGGAAAGAGGAAAGTCACTTTTGTTTAAGACCTCTGCAGGTGTCAACATGTGCACCCTTATTGCGATGGATTTGGGAGAGTTATGTGAGGACACAATGACCTACAAATGCCCCCGGATCACTGAGGCGGAACCAGATGACGTTGACTGTTGGTGCAATGCCACGGACACATGGGTGACCTATGGAACGTGTTCTCAAACTGGCGAACACCGACGAGACAAACGTTCCGTCGCACTGGCCCCACACGTGGGGCTTGGTCTAGAAACAAGAACCGAAACGTGGATGTCCTCTGAAGGCGCTTGGAAACAAATACAAAAAGTGGAGACTTGGGCTCTGAGACACCCAGGATTCACGGTGATAGCCCTTTTTCTAGCACATGCCATAGGAACATCCATCACCCAGAAAGGGATTATTTTCATTTTGCTGATGCTGGTAACACCATCCATGGCCATGCGATGCGTGGGAATAGGCAACAGAGACTTCGTGGAAGGACTGTCAGGAGCAACGTGGGTGGATGTGGTACTGGAGCATGGAAGTTGCGTCACCACCATGGCAAAAAATAAACCAACATTGGACATTGAACTCTTGAAGACGGAGGTCACAAACCCTGCCGTCCTGCGCAAACTGTGCATTGAAGCTAAAATATCAAACACCACCACCGATTCAAGATGTCCAACACAAGGAGAAGCCACACTGGTGGAAGAACAAGACGCGAACTTTGTGTGTCGACGAACGTTCGTGGACAGAGGCTGGGGCAATGGCTGTGGGCTATTCGGAAAAGGTAGCCTAATAACGTGTGCTAAGTTCAAGTGTGTGACAAAACTAGAAGGAAAGATAGTTCAATATGAAAACTTAAAATATTCAGTGATAGTCACCGTCCACACTGGAGACCAGCACCAGGTGGGAAATGAGACCACAGAACATGGAACAACTGCAACCATAACACCTCAAGCTCCTACGTCGGAAATACAGCTGACCGACTACGGAGCCCTTACATTGGATTGCTCACCTAGAACAGGGCTAGACTTTAATGAGATGGTGTTGTTGACAATGAAAGAAAAATCATGGCTTGTCCACAAACAATGGTTTCTAGACTTACCACTGCCTTGGACCTCGGGGGCTTCAACATCCCAAGAGACTTGGAACAGACAAGATTTGCTGGTCACATTTAAGACAGCTCATGCAAAGAAGCAGGAAGTAGTCGTACTAGGATCACAAGAAGGAGCAATGCACACTGCGTTGACTGGAGCGACAGAAATCCAAACGTCAGGAACGACAACAATTTTTGCAGGACACCTGAAATGCAGACTAAAAATGGACAAACTGACTTTAAAAGGGATGTCATATGTGATGTGCACAGGCTCATTCAAGTTAGAGAAAGAAGTGGCTGAGACCCAGCATGGAACTGTTCTAGTGCAGGTTAAATACGAAGGAACAGATGCACCATGCAAGATCCCCTTTTCGACCCAAGATGAGAAAGGAGTAACCCAGAATGGGAGATTGATAACAGCCAACCCCATAGTCACTGACAAAGAAAAACCAGTCAACATTGAGGCAGAACCACCTTTTGGTGAGAGCTACATCGTGGTAGGAGCAGGTGAAAAAGCTTTGAAACTAAGCTGGTTCAAGAAAGGAAGCAGCATAGGGAAAATGTTTGAAGCAACTGCCCGAGGAGCACGAAGGATGGCCATCCTGGGAGACACCGCATGGGACTTCGGTTCTATAGGAGGAGTGTTCACGTCTGTGGGAAAACTGGTACACCAGGTTTTTGGAACTGCATATGGAGTTTTGTTCAGCGGTGTTTCTTGGACCATGAAAATAGGAATAGGGATTCTGCTGACATGGCTAGGATTAAATTCAAGGAGCACGTCCCTTTCGATGACGTGCATTGCAGTTGGCATGGTCACACTGTACCTAGGAGTCATGGTTCAGGCGGACTCGGGATGTGTAATCAACTGGAAAGGCAGAGAACTCAAATGTGGAAGTGGCATTTTTGTCACTAATGAAGTTCACACTTGGACAGAGCAATACAAATTCCAGGCTGACTCCCCAAAGAGACTATCAGCAGCCATTGGGAAGGCATGGGAGGAGGGTGTGTGTGGAATTCGATCAGCCACTCGTCTCGAGAACATCATGTGGAAGCAAATATCAAATGAATTGAACCACATCCTACTTGAAAATGACATGAAATTCACAGTGGTCGTAGGAGATGTTAGTGGAATCTTGGCCCAAGGAAAAAAAATGATTAGGCCACAACCCATGGAACACAAATACTCGTGGAAAAGCTGGGGAAAAGCCAAAATCATAGGAGCAGATGTACAGAACACCACCTTCATCATCGACGGCCCAAACACCCCAGAATGCCCTGATGACCAAAGAGCATGGAACATTTGGGAAGTTGAGGACTATGGATTTGGAATTTTCACGACAAACATATGGTTGAAATTGCGTGACTCCTACACCCAAGTGTGTGACCACCGGCTAATGTCAGCTGCCATCAAGGACAGCAAGGCAGTCCATGCTGACATGGGGTACTGGATAGAAAGTGAAAAGAACGAGACCTGGAAGCTGGCGAGAGCCTCCTTCATAGAAGTTAAGACATGCATCTGGCCAAAATCCCACACTCTATGGAGCAATGGAGTTCTGGAAAGTGAAATGATAATCCCAAAGATATATGGAGGACCAATATCTCAGCACAACTACAGACCAGGATATTTCACACAAACAGCAGGGCCGTGGCACCTAGGCAAGTTGGAACTAGATTTTGATTTGTGTGAAGGTACCACAGTTGTTGTGGATGAACATTGTGGAAATCGAGGACCATCTCTTAGAACCACAACAGTCACAGGAAAGATAATCCATGAATGGTGCTGCAGATCTTGTACGCTACCCCCCTTACGTTTCAAAGGAGAAGACGGGTGTTGGTACGGCATGGAAATCAGACCAGTCAAGGAGAAGGAAGAGAACCTAGTCAAGTCAATGGTCTCTGCAGGGTCAGGAGAAGTGGACAGCTTTTCACTAGGACTGCTATGCATATCAATAATGATTGAAGAGGTGATGAGATCCAGATGGAGTAGAAAAATGCTGATGACTGGAACACTGGCTGTGTTCCTCCTTCTTATAATGGGACAATTGACATGGAATGATCTGATCAGGTTATGCATCATGGTTGGAGCCAATGCTTCAGACAGGATGGGGATGGGAACAACGTACCTAGCTTTGATGGCCACTTTCAAAATGAGACCAATGTTCGCTGTCGGGCTATTATTTCGCAGACTAACATCTAGAGAAGTTCTTCTTCTTACAATTGGATTGAGCCTGGTGGCATCCGTGGAGCTACCAAATTCCTTAGAGGAGCTGGGGGATGGACTTGCAATGGGCATCATGATGTTAAAATTACTGACTGATTTTCAGTCACACCAGCTATGGGCTACCTTGCTGTCCTTGACATTTATCAAAACAACTTTTTCATTGCACTATGCATGGAAGACAATGGCTATGGTACTGTCAATTGTATCTCTCTTCCCTTTATGCCTGTCCACGACCTCTCAAAAAACAACATGGCTTCCGGTGCTGTTGGGATCTCTTGGATGCAAACCACTAACCATGTTTCTTATAACAGAAAACAAAATCTGGGGAAGGAAAAGTTGGCCCCTCAATGAAGGAATTATGGCTGTTGGAATAGTTAGCATTCTACTAAGTTCACTCCTCAAAAATGATGTGCCGCTAGCCGGCCCACTAATAGCTGGAGGCATGCTAATAGCATGTTATGTCATATCCGGAAGCTCAGCCGATTTATCACTGGAGAAAGCGGCTGAGGTCTCCTGGGAAGAAGAAGCAGAACACTCTGGTGCCTCACACAACATACTAGTGGAGGTCCAAGATGATGGAACCATGAAGATAAAAGATGAAGAGAGAGATGACACACTCACCATTCTCCTTAAAGCAACTCTGCTGGCAGTCTCAGGGGTGTACCCAATGTCAATACCAGCGACCCTTTTTGTGTGGTATTTTTGGCAGAAAAAGAAACAGAGATCAGGAGTGCTATGGGACACACCCAGCCCTCCAGAAGTGGAAAGAGCAGTTCTTGATGATGGTATCTATAGAATTTTGCAAAGAGGACTGTTGGGCAGGTCCCAAGTAGGAGTAGGAGTTTTCCAAGAAGGCGTGTTCCACACAATGTGGCACGTCACCAGGGGAGCTGTCCTCATGTATCAAGGGAAGAGGCTGGAACCAAGCTGGGCCAGTGTCAAAAAAGACTTGATCTCATATGGAGGAGGTTGGAGGTTTCAAGGATCCTGGAACACGGGAGAAGAAGTGCAGGTGATTGCTGTTGAACCGGGAAAAAACCCCAAAAATGTACAGACAGCGCCGGGCACCTTCAAGACCCCTGAAGGCGAAGTTGGAGCCATAGCCCTAGATTTTAAACCCGGCACATCTGGATCTCCCATCGTGAACAGAGAGGGAAAAATAGTAGGTCTTTATGGAAATGGAGTGGTGACAACAAGTGGAACCTACGTCAGTGCCATAGCTCAAGCTAAAGCATCACAAGAAGGGCCTCTACCAGAGATTGAGGACGAGGTGTTTAGGAAAAGAAACTTAACAATAATGGACCTACATCCAGGATCGGGAAAAACAAGAAGATATCTTCCAGCCATAGTCCGTGAGGCCATAAAAAGGAAGCTGCGCACGCTAATCTTGGCTCCCACAAGAGTTGTCGCTTCTGAAATGGCAGAGGCGCTCAAGGGAATGCCAATAAGGTATCAGACAACAGCAGTGAAGAGTGAACACACAGGAAAGGAGATAGTTGACCTTATGTGCCACGCCACTTTCACCATGCGTCTCCTGTCTCCCGTGAGAGTTCCCAATTACAACATGATTATCATGGATGAAGCACATTTCACCGATCCAGCCAGCATAGCGGCCAGAGGGTACATCTCAACCCGAGTGGGTATGGGTGAAGCAGCTGCGATCTTTATGACAGCCACTCCCCCAGGATCGGTGGAGGCCTTTCCACAGAGCAATGCAGTTATCCAAGATGAGGAAAGAGACATTCCTGAGAGATCATGGAACTCAGGCTATGACTGGATCACTGATTTCCCAGGTAAAACAGTCTGGTTTGTTCCAAGCATCAAATCAGGAAATGACATTGCCAACTGTTTAAGAAAGAACGGGAAACGGGTGATCCAATTGAGCAGAAAAACCTTTGACACTGAGTACCAGAAAACAAAAAACAACGACTGGGACTATGTCGTCACAACAGACATTTCCGAAATGGGAGCAAACTTCCGGGCCGACAGGGTAATAGACCCAAGGCGGTGTCTGAAACCGGTAATACTAAAAGATGGTCCAGAGCGCGTCATTCTAGCCGGACCGATGCCAGTGACTGTGGCCAGTGCCGCCCAGAGGAGAGGAAGAATTGGAAGGAACCAAAACAAGGAAGGTGATCAGTATATTTACATGGGACAGCCTTTAAACAATGATGAGGACCACGCTCATTGGACAGAAGCAAAAATGCTCCTTGACAATATAAACACACCAGAAGGGATTATCCCAGCCCTCTTTGAGCCGGAGAGAGAAAAGAGTGCAGCAATAGACGGGGAATACAGACTGCGGGGTGAAGCAAGGAAAACGTTCGTGGAGCTCATGAGAAGAGGAGATCTACCTGTCTGGCTATCCTACAAAGTTGCCTCAGAAGGCTTCCAGTACTCCGACAGAAGGTGGTGCTTTGATGGGGAAAGGAACAACCAGGTGTTGGAGGAGAACATGGACGTGGAGATCTGGACAAAAGAAGGAGAAAGAAAGAAACTACGACCCCGCTGGTTGGATGCCAGAACATACTCTGACCCACTGGCTCTGCGCGAGTTTAAAGAGTTTGCAGCAGGAAGAAGAAGCGTCTCAGGTGACCTAATATTAGAAATAGGGAAACTTCCACAACATTTGACGCAAAGGGCCCAGAATGCTTTGGACAACTTGGTCATGTTGCACAATTCCGAACAAGGAGGAAAAGCCTATAGACATGCTATGGAAGAACTACCAGACACCATAGAAACGTTGATGCTCCTAGCTTTGATAGCTGTGTTGACTGGTGGAGTGACGCTGTTCTTCCTATCAGGAAGAGGTCTAGGGAAAACATCCATCGGCCTACTCTGCGTGATGGCCTCAAGCGTACTGTTATGGATGGCCAGTGTGGAGCCCCATTGGATAGCGGCCTCCATCATACTGGAGTTCTTTCTGATGGTGCTGCTTATTCCAGAGCCAGACAGACAGCGCACTCCACAGGACAACCAGCTAGCATATGTGGTGATAGGTTTGTTATTCATGATATTGACAGTGGCAGCCAATGAGATGGGATTATTGGAAACCACAAAGAAAGACCTGGGGATTGGCCATGTAGCTGCTGAAAACCACCACCATGCTACAATGCTGGACGTAGACCTACATCCAGCTTCAGCCTGGACCCTCTATGCAGTGGCCACAACAATTATCACTCCCATGATGAGACACACAATTGAAAACACAACGGCAAATATTTCCCTGACAGCTATTGCAAACCAGGCAGCTATATTGATGGGACTTGACAAGGGATGGCCAATATCGAAGATGGACATAGGAGTTCCACTTCTCGCCTTGGGGTGCTATTCCCAGGTGAACCCGCTGACGCTGACAGCGGCGGTATTGATGCTAGTGGCTCATTACGCCATAATTGGACCTGGACTGCAAGCAAAAGCTACTAGAGAAGCTCAAAAAAGGACAGCGGCCGGAATAATGAAAAATCCAACTGTCGACGGGATTGTTGCAATAGATTTGGATCCTGTGGTTTACGATGCAAAATTTGAAAAACAGCTAGGCCAAATAATGTTGTTGATACTTTGCACATCACAGATTCTCTTGATGCGGACTACATGGGCCTTGTGTGAATCCATCACACTGGCTACTGGACCTCTGACCACTCTTTGGGAGGGATCTCCAGGAAAATTCTGGAACACCACGATAGCGGTGTCCATGGCAAACATTTTCAGGGGAAGTTATCTAGCAGGAGCAGGTCTGGCCTTCTCATTAATGAAATCTCTAGGAGGAGGTAGGAGAGGCACGGGAGCCCAAGGGGAAACACTGGGAGAAAAATGGAAAAGACAGCTAAACCAACTGAGCAAGTCAGAATTCAACACTTACAAAAGGAGTGGGATTATGGAGGTGGATAGATCCGAAGCCAAAGAGGGACTGAAAAGAGGAGAAACAACCAAACATGCAGTGTCGAGAGGAACAGCCAAACTGAGGTGGTTTGTGGAGAGGAACCTTGTGAAACCAGAAGGGAAAGTCATAGACCTCGGTTGTGGAAGAGGTGGCTGGTCATATTATTGCGCTGGGCTGAAGAAAGTCACAGAAGTGAAAGGATACACAAAAGGAGGACCTGGACATGAGGAACCAATCCCAATGGCGACCTATGGATGGAACCTAGTAAAGCTACACTCCGGAAAAGATGTATTCTTTACACCACCTGAGAAATGTGACACCCTTTTGTGTGATATTGGTGAGTCCTCTCCGAACCCAACTATAGAAGAAGGAAGAACGTTACGTGTTCTAAAGATGGTGGAACCATGGCTCAGAGGAAACCAATTTTGCATAAAAATTCTAAATCCCTATATGCCGAGTGTGGTAGAAACTCTGGAGCAAATGCAAAGAAAACATGGAGGAATGCTAGTGCGAAACCCACTCTCAAGAAATTCCACCCATGAAATGTACTGGGTTTCATGTGGAACAGGAAACATTGTGTCAGCAGTAAACATGACATCTAGAATGTTGCTAAATCGATTCACAATGGCTCACAGGAAGCCAACATATGAAAGAGACGTGGACTTAGGCGCTGGAACAAGACATGTGGCAGTGGAACCAGAGGTAGCCAACCTAGATATCATTGGCCAGAGGATAGAGAATATAAAAAATGAACATAAGTCAACATGGCATTATGATGAGGACAATCCATACAAAACATGGGCCTATCATGGATCATATGAGGTCAAGCCATCAGGATCAGCCTCATCCATGGTCAATGGCGTGGTGAGATTGCTCACCAAACCATGGGATGTTATCCCCATGGTCACACAAATAGCCATGACTGACACCACACCCTTTGGACAACAGAGGGTGTTTAAAGAGAAAGTTGACACGCGCACACCAAAAGCAAAACGAGGCACAGCACAAATTATGGAGGTGACAGCCAGGTGGTTATGGGGTTTCCTTTCTAGAAACAAAAAACCCAGAATCTGCACAAGAGAGGAGTTCACAAGAAAAGTTAGGTCAAACGCAGCTATTGGAGCAGTGTTCGTTGATGAAAATCAATGGAACTCAGCAAAAGAAGCAGTGGAAGACGAACGGTTCTGGGACCTTGTGCACAGAGAGAGGGAGCTTCATAAACAGGGAAAATGTGCCACGTGTGTCTACAATATGATGGGGAAGAGAGAGAAAAAATTAGGAGAGTTCGGAAAGGCAAAAGGAAGTCGTGCAATATGGTACATGTGGTTGGGAGCACGCTTTCTAGAGTTCGAAGCCCTTGGTTTCATGAATGAAGATCACTGGTTCAGTAGAGAGAATTCACTCAGTGGAGTGGAAGGAGAAGGACTCCACAAACTTGGATACATACTCAGAGACATATCAAAGATTCCAGGGGGAAATATGTATGCAGATGACACAGCCGGATGGGACACAAGAATAACAGAGGATGATCTTCAGAATGAGGCTAAAATCACTGACATCATGGAGCCCGAACATGCCCTATTGGCTACGTCAATCTTTAAGCTGACCTACCAAAATAAGGTGGTAAGGGTGCAGAGACCAGCAAAAAATGGAACCGTGATGGATGTTATATCCAGACGTGACCAGAGAGGAAGTGGACAGGTCGGAACTTATGGCTTAAACACTTTCACCAACATGGAGGCCCAACTAATAAGACAAATGGAGTCTGAGGGAATCTTTTTACCCAGCGAATTGGAAACCCCAAATCTAGCCGAAAGAGTTCTCGACTGGTTGGAAAAACATGGCGTCGAAAGGCTGAAAAGAATGGCAATCAGCGGAGATGACTGTGTGGTGAAACCAATTGATGACAGGTTCGCAACAGCCTTAACAGCTTTGAATGACATGGGAAAAGTAAGAAAAGACATACCGCAATGGGAACCTTCAAAAGGATGGAATGATTGGCAACAAGTGCCTTTCTGTTCACACCATTTCCACCAGCTGATTATGAAGGATGGGAGGGAGATAGTGGTGCCATGCCGCAACCAAGATGAACTTGTGGGTAGGGCCAGAGTATCACAAGGCGCCGGATGGAGCCTGAGAGAAACTGCATGCCTAGGCAAGTCATATGCACAAATGTGGCAGCTGATGTACTTCCACAGGAGAGACCTGAGACTAGCGGCTAATGCTATCTGTTCAGCCGTTCCAGTTGATTGGGTCCCAACCAGCCGCACCACCTGGTCGATCCATGCCCATCACCAATGGATGACAACAGAAGACATGTTATCAGTGTGGAATAGGGTTTGGATAGAGGAAAACCCATGGATGGAGGATAAAACTCATGTATCCAGTTGGGAAGATGTTCCATACTTAGGAAAAAGGGAAGATCAGTGGTGTGGATCCCTGATAGGCTTAACAGCAAGGGCCACCTGGGCCACTAACATACAAGTGGCCATAAACCAAGTGAGAAGGCTCATTGGGAATGAGAATTATCTAGATTACATGACATCAATGAAGAGATTCAAGAATGAGAGTGATCCCGAAGGGGCACTCTGGTAAGTCAACACATTCACAAAATAAAGGAAAATAAAAAATCAAACAAGGCAAGAAGTCAGGCCGGATTAAGCCATAGTACGGTAAGAGCTATGCTGCCTGTGAGCCCCGTCCAAGGACGTAAAATGAAGTCAGGCCGAAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTGGCTCCATCGTGGGGATGTAAAAACCCGGGAGGCTGCAACCCATGGAAGCTGTACGCATGGGGTAGCAGACTAGTGGTTAGAGGAGACCCCTCCCAAGACACAACGCAGCAGCGGGGCCCAACACCAGGGGAAGCTGTACCCTGGTGGTAAGGACTAGAGGTTAGAGGAGACCCCCCGCACAACAATAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCTACAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/resources/denv2/genome_annotation.gff3 b/nextclade/resources/denv2/genome_annotation.gff3 index 1f350fbc..40026b43 100644 --- a/nextclade/resources/denv2/genome_annotation.gff3 +++ b/nextclade/resources/denv2/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_001474.2 1 10723 -NC_001474.2 feature gene 97 438 . + . codon_start=1;gene=C;gene_name=C; -NC_001474.2 feature gene 439 711 . + . codon_start=1;gene=pr;gene_name=pr; -NC_001474.2 feature gene 439 936 . + . codon_start=1;gene=M;gene_name=M; -NC_001474.2 feature gene 937 2421 . + . codon_start=1;gene=E;gene_name=E; -NC_001474.2 feature gene 2422 3477 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_001474.2 feature gene 3478 4131 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_001474.2 feature gene 4132 4521 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_001474.2 feature gene 4522 6375 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_001474.2 feature gene 6376 6756 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_001474.2 feature gene 6757 6825 . + . codon_start=1;gene=2K;gene_name=2K; -NC_001474.2 feature gene 6826 7569 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_001474.2 feature gene 7570 10269 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome 1 10723 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 97 438 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 439 711 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 439 936 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 937 2421 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 2422 3477 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 3478 4131 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 4132 4521 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 4522 6375 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 6376 6756 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 6757 6825 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 6826 7569 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome feature gene 7570 10269 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/resources/denv2/pathogen.json b/nextclade/resources/denv2/pathogen.json index b968b789..a1cac1fd 100644 --- a/nextclade/resources/denv2/pathogen.json +++ b/nextclade/resources/denv2/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/resources/denv2/reference.fasta b/nextclade/resources/denv2/reference.fasta index 1610f7c4..271ec64d 100644 --- a/nextclade/resources/denv2/reference.fasta +++ b/nextclade/resources/denv2/reference.fasta @@ -1,180 +1,2 @@ ->NC_001474.2 Dengue virus 2, complete genome -AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAACGTA -GTTCTAACAGTTTTTTAATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCG -AAAAACACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAG -CTGACAAAGAGATTCTCACTTGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATG -GCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATATTGAAGAGA -TGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAGGAAAGAGATT -GGAAGGATGCTGAACATCTTGAATAGGAGACGCAGATCTGCAGGCATGATCATTATGCTG -ATTCCAACAGTGATGGCGTTCCATTTAACCACACGTAACGGAGAACCACACATGATCGTC -AGCAGACAAGAGAAAGGGAAAAGTCTTCTGTTTAAAACAGAGGATGGCGTGAACATGTGT -ACCCTCATGGCCATGGACCTTGGTGAATTGTGTGAAGACACAATCACGTACAAGTGTCCC -CTTCTCAGGCAGAATGAGCCAGAAGACATAGACTGTTGGTGCAACTCTACGTCCACGTGG -GTAACTTATGGGACGTGTACCACCATGGGAGAACATAGAAGAGAAAAAAGATCAGTGGCA -CTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAA -GGGGCCTGGAAACATGTCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTCACC -ATGATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATT -TTCATCTTACTGACAGCTGTCACTCCTTCAATGACAATGCGTTGCATAGGAATGTCAAAT -AGAGACTTTGTGGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGA -AGCTGTGTGACGACGATGGCAAAAAACAAACCAACATTGGATTTTGAACTGATAAAAACA -GAAGCCAAACAGCCTGCCACCCTAAGGAAGTACTGTATAGAGGCAAAGCTAACCAACACA -ACAACAGAATCTCGCTGCCCAACACAAGGGGAACCCAGCCTAAATGAAGAGCAGGACAAA -AGGTTCGTCTGCAAACACTCCATGGTAGACAGAGGATGGGGAAATGGATGTGGACTATTT -GGAAAGGGAGGCATTGTGACCTGTGCTATGTTCAGATGCAAAAAGAACATGGAAGGAAAA -GTTGTGCAACCAGAAAACTTGGAATACACCATTGTGATAACACCTCACTCAGGGGAAGAG -CATGCAGTCGGAAATGACACAGGAAAACATGGCAAGGAAATCAAAATAACACCACAGAGT -TCCATCACAGAAGCAGAATTGACAGGTTATGGCACTGTCACAATGGAGTGCTCTCCAAGA -ACGGGCCTCGACTTCAATGAGATGGTGTTGCTGCAGATGGAAAATAAAGCTTGGCTGGTG -CACAGGCAATGGTTCCTAGACCTGCCGTTACCATGGTTGCCCGGAGCGGACACACAAGGG -TCAAATTGGATACAGAAAGAGACATTGGTCACTTTCAAAAATCCCCATGCGAAGAAACAG -GATGTTGTTGTTTTAGGATCCCAAGAAGGGGCCATGCACACAGCACTTACAGGGGCCACA -GAAATCCAAATGTCATCAGGAAACTTACTCTTCACAGGACATCTCAAGTGCAGGCTGAGA -ATGGACAAGCTACAGCTCAAAGGAATGTCATACTCTATGTGCACAGGAAAGTTTAAAGTT -GTGAAGGAAATAGCAGAAACACAACATGGAACAATAGTTATCAGAGTGCAATATGAAGGG -GACGGCTCTCCATGCAAGATCCCTTTTGAGATAATGGATTTGGAAAAAAGACATGTCTTA -GGTCGCCTGATTACAGTCAACCCAATTGTGACAGAAAAAGATAGCCCAGTCAACATAGAA -GCAGAACCTCCATTCGGAGACAGCTACATCATCATAGGAGTAGAGCCGGGACAACTGAAG -CTCAACTGGTTTAAGAAAGGAAGTTCTATCGGCCAAATGTTTGAGACAACAATGAGGGGG -GCGAAGAGAATGGCCATTTTAGGTGACACAGCCTGGGATTTTGGATCCTTGGGAGGAGTG -TTTACATCTATAGGAAAGGCTCTCCACCAAGTCTTTGGAGCAATCTATGGAGCTGCCTTC -AGTGGGGTTTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATG -AATTCACGCAGCACCTCACTGTCTGTGACACTAGTATTGGTGGGAATTGTGACACTGTAT -TTGGGAGTCATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTG -AAATGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGGACAGAACAATACAAG -TTCCAACCAGAATCCCCTTCAAAACTAGCTTCAGCTATCCAGAAAGCCCATGAAGAGGGC -ATTTGTGGAATCCGCTCAGTAACAAGACTGGAGAATCTGATGTGGAAACAAATAACACCA -GAATTGAATCACATTCTATCAGAAAATGAGGTGAAGTTAACTATTATGACAGGAGACATC -AAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCTCAGCCCACTGAGCTGAAGTAT -TCATGGAAAACATGGGGCAAAGCAAAAATGCTCTCTACAGAGTCTCATAACCAGACCTTT -CTCATTGATGGCCCCGAAACAGCAGAATGCCCCAACACAAATAGAGCTTGGAATTCGTTG -GAAGTTGAAGACTATGGCTTTGGAGTATTCACCACCAATATATGGCTAAAATTGAAAGAA -AAACAGGATGTATTCTGCGACTCAAAACTCATGTCAGCGGCCATAAAAGACAACAGAGCC -GTCCATGCCGATATGGGTTATTGGATAGAAAGTGCACTCAATGACACATGGAAGATAGAG -AAAGCCTCTTTCATTGAAGTTAAAAACTGCCACTGGCCAAAATCACACACCCTCTGGAGC -AATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATCTCGCTGGACCAGTGTCTCAA -CACAACTATAGACCAGGCTACCATACACAAATAACAGGACCATGGCATCTAGGTAAGCTT -GAGATGGACTTTGATTTCTGTGATGGAACAACAGTGGTAGTGACTGAGGACTGCGGAAAT -AGAGGACCCTCTTTGAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGC -CGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGGTGCTGGTACGGGATG -GAAATCAGACCATTGAAGGAGAAAGAAGAGAATTTGGTCAACTCCTTGGTCACAGCTGGA -CATGGGCAGGTCGACAACTTTTCACTAGGAGTCTTGGGAATGGCATTGTTCCTGGAGGAA -ATGCTTAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTTGTG -ACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTAGGC -GCCACTATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCCTACTAGCAGCCTTC -AAAGTCAGACCAACTTTTGCAGCTGGACTACTCTTGAGAAAGCTGACCTCCAAGGAATTG -ATGATGACTACTATAGGAATTGTACTCCTCTCCCAGAGCACCATACCAGAGACCATTCTT -GAGTTGACTGATGCGTTAGCCTTAGGCATGATGGTCCTCAAAATGGTGAGAAATATGGAA -AAGTATCAATTGGCAGTGACTATCATGGCTATCTTGTGCGTCCCAAACGCAGTGATATTA -CAAAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCCGTTTCCCCACTGCTC -TTAACATCCTCACAGCAAAAAACAGATTGGATACCATTAGCATTGACGATCAAAGGTCTC -AATCCAACAGCTATTTTTCTAACAACCCTCTCAAGAACCAGCAAGAAAAGGAGCTGGCCA -TTAAATGAGGCTATCATGGCAGTCGGGATGGTGAGCATTTTAGCCAGTTCTCTCCTAAAA -AATGATATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTG -CTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCAGCCGATGTCAAATGGGAAGAC -CAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGC -ATGTCGATAAAAAATGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTG -CTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTG -TGGGAAGTGAAGAAACAACGGGCCGGAGTATTGTGGGATGTTCCTTCACCCCCACCCATG -GGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATTAAGCAAAAAGGGATTCTTGGATAT -TCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCATACAATGTGGCATGTCACA -CGTGGCGCTGTTCTAATGCATAAAGGAAAGAGGATTGAACCATCATGGGCGGACGTCAAG -AAAGACCTAATATCATATGGAGGAGGCTGGAAGTTAGAAGGAGAATGGAAGGAAGGAGAA -GAAGTCCAGGTATTGGCACTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACGAAACCT -GGTCTTTTCAAAACCAACGCCGGAACAATAGGTGCTGTATCTCTGGACTTTTCTCCTGGA -ACGTCAGGATCTCCAATTATCGACAAAAAAGGAAAAGTTGTGGGTCTTTATGGTAATGGT -GTTGTTACAAGGAGTGGAGCATATGTGAGTGCTATAGCCCAGACTGAAAAAAGCATTGAA -GACAACCCAGAGATCGAAGATGACATTTTCCGAAAGAGAAGACTGACCATCATGGACCTC -CACCCAGGAGCGGGAAAGACGAAGAGATACCTTCCGGCCATAGTCAGAGAAGCTATAAAA -CGGGGTTTGAGAACATTAATCTTGGCCCCCACTAGAGTTGTGGCAGCTGAAATGGAGGAA -GCCCTTAGAGGACTTCCAATAAGATACCAGACCCCAGCCATCAGAGCTGAGCACACCGGG -CGGGAGATTGTGGACCTAATGTGTCATGCCACATTTACCATGAGGCTGCTATCACCAGTT -AGAGTGCCAAACTACAACCTGATTATCATGGACGAAGCCCATTTCACAGACCCAGCAAGT -ATAGCAGCTAGAGGATACATCTCAACTCGAGTGGAGATGGGTGAGGCAGCTGGGATTTTT -ATGACAGCCACTCCCCCGGGAAGCAGAGACCCATTTCCTCAGAGCAATGCACCAATCATA -GATGAAGAAAGAGAAATCCCTGAACGTTCGTGGAATTCCGGACATGAATGGGTCACGGAT -TTTAAAGGGAAGACTGTTTGGTTCGTTCCAAGTATAAAAGCAGGAAATGATATAGCAGCT -TGCCTGAGGAAAAATGGAAAGAAAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAG -TATGTCAAGACTAGAACCAATGATTGGGACTTCGTGGTTACAACTGACATTTCAGAAATG -GGTGCCAATTTCAAGGCTGAGAGGGTTATAGACCCCAGACGCTGCATGAAACCAGTCATA -CTAACAGATGGTGAAGAGCGGGTGATTCTGGCAGGACCTATGCCAGTGACCCACTCTAGT -GCAGCACAAAGAAGAGGGAGAATAGGAAGAAATCCAAAAAATGAGAATGACCAGTACATA -TACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAAGAAGCTAAAATG -CTCCTAGATAACATCAACACGCCAGAAGGAATCATTCCTAGCATGTTCGAACCAGAGCGT -GAAAAGGTGGATGCCATTGATGGCGAATACCGCTTGAGAGGAGAAGCAAGGAAAACCTTT -GTAGACTTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCCTACAGAGTGGCAGCTGAA -GGCATCAACTACGCAGACAGAAGGTGGTGTTTTGATGGAGTCAAGAACAACCAAATCCTA -GAAGAAAACGTGGAAGTTGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTGAAACCC -AGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTTAAGGAATTT -GCAGCCGGAAGAAAGTCTCTGACCCTGAACCTAATCACAGAAATGGGTAGGCTCCCAACC -TTCATGACTCAGAAGGCAAGAGACGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAG -GCAGGTGGAAGGGCGTACAACCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTG -CTTTTACTGACACTTCTGGCTACAGTCACGGGAGGGATCTTTTTATTCTTGATGAGCGGA -AGGGGCATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCTAGCATCCTCCTA -TGGTACGCACAAATACAGCCACACTGGATAGCAGCTTCAATAATACTGGAGTTTTTTCTC -ATAGTTTTGCTTATTCCAGAACCTGAAAAACAGAGAACACCCCAAGACAACCAACTGACC -TACGTTGTCATAGCCATCCTCACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTC -CTAGAAAAAACGAAGAAAGATCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGC -AACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACA -ACATTTGTTACACCAATGTTGAGACATAGCATTGAAAATTCCTCAGTGAATGTGTCCCTA -ACAGCTATAGCCAACCAAGCCACAGTGTTAATGGGTCTCGGGAAAGGATGGCCATTGTCA -AAGATGGACATCGGAGTTCCCCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATA -ACTCTCACAGCAGCTCTTTTCTTATTGGTAGCACATTATGCCATCATAGGGCCAGGACTC -CAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGCAGCGGCGGGCATCATGAAAAACCCA -ACTGTCGATGGAATAACAGTGATTGACCTAGATCCAATACCTTATGATCCAAAGTTTGAA -AAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTATTGATGATGAGG -ACTACATGGGCTCTGTGTGAGGCTTTAACCTTAGCTACCGGGCCCATCTCCACATTGTGG -GAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCGGTGTCAATGGCTAACATTTTT -AGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCTATTATGAAGAACACAACCAAC -ACAAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAATGGAAAAGCCGATTG -AACGCATTGGGAAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGAT -AGAACCTTAGCAAAAGAAGGCATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGA -GGCTCAGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCACACCAGAAGGGAAAGTA -GTGGACCTCGGTTGTGGCAGAGGAGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTA -AGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAACCCATCCCCATGTCA -ACATATGGGTGGAATCTAGTGCGTCTTCAAAGTGGAGTTGACGTTTTCTTCATCCCGCCA -GAAAAGTGTGACACATTATTGTGTGACATAGGGGAGTCATCACCAAATCCCACAGTGGAA -GCAGGACGAACACTCAGAGTCCTTAACTTAGTAGAAAATTGGTTGAACAACAACACTCAA -TTTTGCATAAAGGTTCTCAACCCATATATGCCCTCAGTCATAGAAAAAATGGAAGCACTA -CAAAGGAAATATGGAGGAGCCTTAGTGAGGAATCCACTCTCACGAAACTCCACACATGAG -ATGTACTGGGTATCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGG -ATGTTGATCAACAGATTTACAATGAGATACAAGAAAGCCACTTACGAGCCGGATGTTGAC -CTCGGAAGCGGAACCCGTAACATCGGGATTGAAAGTGAGATACCAAACCTAGATATAATT -GGGAAAAGAATAGAAAAAATAAAGCAAGAGCATGAAACATCATGGCACTATGACCAAGAC -CACCCATACAAAACGTGGGCATACCATGGTAGCTATGAAACAAAACAGACTGGATCAGCA -TCATCCATGGTCAACGGAGTGGTCAGGCTGCTGACAAAACCTTGGGACGTCGTCCCCATG -GTGACACAGATGGCAATGACAGACACGACTCCATTTGGACAACAGCGCGTTTTTAAAGAG -AAAGTGGACACGAGAACCCAAGAACCGAAAGAAGGCACGAAGAAACTAATGAAAATAACA -GCAGAGTGGCTTTGGAAAGAATTAGGGAAGAAAAAGACACCCAGGATGTGCACCAGAGAA -GAATTCACAAGAAAGGTGAGAAGCAATGCAGCCTTGGGGGCCATATTCACTGATGAGAAC -AAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATAGTAGGTTTTGGGAGCTGGTTGACAAG -GAAAGGAATCTCCATCTTGAAGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAA -AGAGAGAAGAAGCTAGGGGAATTCGGCAAGGCAAAAGGCAGCAGAGCCATATGGTACATG -TGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTAAATGAAGATCACTGG -TTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGCACAAGCTAGGTTAC -ATTCTAAGAGACGTGAGCAAGAAAGAGGGAGGAGCAATGTATGCCGATGACACCGCAGGA -TGGGATACAAGAATCACACTAGAAGACCTAAAAAATGAAGAAATGGTAACAAACCACATG -GAAGGAGAACACAAGAAACTAGCCGAGGCCATTTTCAAACTAACGTACCAAAACAAGGTG -GTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGACATCATATCGAGAAGAGAC -CAAAGAGGTAGTGGACAAGTTGGCACCTATGGACTCAATACTTTCACCAATATGGAAGCC -CAACTAATCAGACAGATGGAGGGAGAAGGAGTCTTTAAAAGCATTCAGCACCTAACAATC -ACAGAAGAAATCGCTGTGCAAAACTGGTTAGCAAGAGTGGGGCGCGAAAGGTTATCAAGA -ATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTTTAGATGACAGGTTCGCAAGCGCT -TTAACAGCTCTAAATGACATGGGAAAGATTAGGAAAGACATACAACAATGGGAACCTTCA -AGAGGATGGAATGATTGGACACAAGTGCCCTTCTGTTCACACCATTTCCATGAGTTAATC -ATGAAAGACGGTCGCGTACTCGTTGTTCCATGTAGAAACCAAGATGAACTGATTGGCAGA -GCCCGAATCTCCCAAGGAGCAGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCT -TACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGCGACCTCAGGCTGGCGGCAAAT -GCTATTTGCTCGGCAGTACCATCACATTGGGTTCCAACAAGTCGAACAACCTGGTCCATA -CATGCTAAACATGAATGGATGACAACGGAAGACATGCTGACAGTCTGGAACAGGGTGTGG -ATTCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCA -TACTTGGGGAAAAGAGAAGACCAATGGTGCGGCTCATTGATTGGGTTAACAAGCAGGGCC -ACCTGGGCAAAGAACATCCAAGCAGCAATAAATCAAGTTAGATCCCTTATAGGCAATGAA -GAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAAGCAGGA -GTTCTGTGGTAGAAAGCAAAACTAACATGAAACAAGGCTAGAAGTCAGGTCGGATTAAGC -CATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCA -GGCCATCATAAATGCCATAGCTTGAGTAAACTATGCAGCCTGTAGCTCCACCTGAGAAGG -TGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGC -GGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGCGAGATGA -AGCTGTAGTCTCGCTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCGAAACAAAAAACAG -CATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACA -GAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome +AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAACGTAGTTCTAACAGTTTTTTGATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCGAGAAATACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTACAACAGCTGACAAAGAGATTCTCACTTGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATACTGAAAAGATGGGGAACAATCAAAAAATCAAAGGCTATCAATGTCCTGAGAGGGTTCAGGAAAGAGATTGGAAGGATGCTGAACATCTTGAACAGGAGACGCAGAACTGCAGGCATGATCATCATGCTGATTCCAACAGTGATGGCGTTCCATTTGACCACACGCAACGGAGAACCACACATGATTGTCAGTAGACAAGAGAAAGGGAAAAGCCTTCTGTTTAAAACAGAGGATGGTATGAACATGTGTACCCTCATGGCCATGGACCTTGGTGAGTTGTGTGAAGACACAATCACGTACAAGTGTCCTTTTCTCAGGCAGAACGAACCAGAAGACATAGATTGTTGGTGCAACTCCACGTCCACATGGGTAACTTATGGGACATGTACCACCACAGGAGAGCACAGAAGAGAAAAAAGATCAGTGGCACTTGTTCCACACGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGCCCAGAGAATTGAAACTTGGATTCTGAGACATCCAGGCTTTACCATAATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGTCCTGATTTTCATCTTACTGACAGCCGTCGCTCCTTCAATGACAATGCGCTGCATAGGAATATCAAATAGAGACTTTGTGGAAGGAGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGAAGCTGTGTGACGACGATGGCAAAAAACAAACCAACATTGGACTTTGAACTGATAAAAACAGAAGCCAAACAACCTGCCACTCTAAGGAAGTACTGTATAGAGGCTAAACTGACCAACACAACAACAGAATCTCGCTGCCCAACACAAGGGGAACCCAGCCTAAATGAAGAGCAGGACAAAAGGTTCGTCTGCAAACACTCCATGGTAGACAGAGGATGGGGAAATGGATGTGGATTATTTGGAAAAGGAGGCATTGTGACCTGTGCTATGTTCACATGCAAAAAGAACATGGAAGGAAAAGTTGTGCAGCCAGAAAACTTGGAATACACCATTGTGATAACACCTCACTCAGGGGAAGAACATGCAGTCGGAAATGACACAGGAAAACATGGCAAGGAAGTCAAGATAACACCACAGAGCTCCATCACAGAAGCAGAACTGACAGGCTATGGCACTGTCACGATGGAGTGCTCTCCGAGAACGGGCCTCGACTTCAATGAGATGGTGTTGCTGCAAATGGAAAACAAAGCTTGGCTGGTGCACAGACAATGGTTCCTAGACCTACCGTTACCATGGCTGCCCGGAGCAGACACACAAGGATCAAATTGGATACAGAAAGAGACATTGGTCACTTTCAAAAATCCCCATGCGAAAAAACAGGATGTTGTTGTCTTAGGATCCCAAGAGGGGGCCATGCACACAGCACTCACAGGGGCCACAGAAATCCAGATGTCATCAGGAAACTTACTGTTCACAGGACATCTCAAGTGCAGGCTGAGAATGGACAAACTACAGCTCAAAGGGATGTCATACTCTATGTGCACAGGAAAGTTTAAAGTTGTGAAGGAAATAGCAGAAACACAACATGGAACAATAGTCATCAGAGTACAATATGAAGGAGACGGCTCTCCATGCAAGATCCCTTTTGAGATAATGGATTTGGAAAAAAGACATGTCTTAGGTCGCCTGATCACAGTCAACCCAATTGTAACAGAAAAAGACAGCCCAGTCAACATAGAAGCAGAACCTCCATTCGGAGACAGCTACATCATCATAGGAGTGGAACCAGGACAATTGAAGCTCAACTGGTTTAAGAAAGGAAGTTCTATCGGCCAAATGTTTGAGACAACAATGAGAGGAGCGAAAAGAATGGCCATTTTGGGTGACACAGCCTGGGATTTTGGATCCCTGGGAGGAGTGTTCACATCTATAGGAAAGGCTCTCCACCAAGTTTTTGGAGCAATCTATGGGGCTGCCTTCAGTGGGGTCTCATGGACTATGAAGATCCTCATAGGAGTTATCATCACATGGATAGGAATGAATTCACGCAGCACCTCACTGTCTGTGTCACTAGTATTAGTGGGAATCGTGACACTATACTTGGGAGTTATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAGAACAAAGAACTGAAATGTGGCAGTGGGATTTTCGTCACAGACAACGTGCACACATGGACAGAACAATACAAGTTCCAACCAGAATCCCCTTCAAAACTGGCTTCAGCCATCCAGAAAGCTCATGAAGAGGGCATTTGTGGAATCCGCTCAGTAACAAGACTGGAGAATCTGATGTGGAAACAGATAACACCAGAATTGAATCACATTCTATCAGAAAATGAAGTAAAGCTGACCATCATGACAGGAGACATTAAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCCCAACCCACTGAGCTGAGGTATTCATGGAAAACATGGGGCAAAGCGAAAATGCTCTCCACAGAGCTCCATAATCAGACCTTTCTCATTGATGGTCCCGAAACAGCAGAATGCCCCAACACAAACAGAGCTTGGAATTCACTGGAAGTTGAGGACTATGGCTTTGGAGTATTCACCACCAATATATGGCTAAAATTGAGAGAAAAGCAGGATGTATTTTGTGACTCAAAACTCATGTCAGCGGCCATAAAGGACAACAGAGCCGTCCATGCTGATATGGGTTATTGGATAGAAAGCGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAGCTGCCACTGGCCAAAGTCACACACCCTCTGGAGTAATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATTTCGCTGGACCAGTGTCACAACACAACTACAGACCAGGCTATTACACACAAACAGCAGGACCTTGGCATCTAGGCAAGCTTGAGATGGACTTTGATTTCTGCGAAGGAACTACAGTGGTGGTGACCGAGGACTGTGGAAACAGAGGACCCTCTTTAAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGCCGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGATGCTGGTACGGGATGGAAATCAGACCATTGAAAGAGAAAGAAGAGAATCTGGTCAACTCTTTGGTCACAGCCGGACATGGGCAGATTGACAACTTTTCACTAGGAATCTTGGGAATGGCATTGTTCCTGGAAGAAATGCTCAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTCGTGACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTGGGCGCTACCATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCCTACTAGCAGCTTTCAAAGTCAGACCAACCTTTGCAGCTGGACTGCTCTTGAGAAAACTGACCTCCAAGGAATTGATGATGACCACCATAGGAATCGTTCTCCTCTCCCAGAGTAGCATACCAGAGACCATTCTTGAACTGACTGATGCGTTAGCCTTGGGCATGATGGTCCTCAAAATAGTGAGAAACATGGAAAAATATCAGCTGGCAGTGACCATCATGGCTATCTTATGCGTCCCAAATGCTGTGATATTACAGAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCTGTTTCCCCACTGCTCTTAACATCCTCACAACAGAAAGCGGATTGGATACCATTAGCATTGACGATCAAAGGTCTCAATCCAACAGCCATTTTTCTAACAACCCTTTCAAGAACCAGCAAGAAAAGGAGCTGGCCTCTAAATGAGGCTATCATGGCAGTTGGGATGGTGAGCATTTTAGCCAGTTCTCTCTTAAAGAATGACATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCCGCCGATGTCAAATGGGAAGATCAGGCAGAGATATCAGGGAGCAGTCCAATTCTGTCAATAACAATATCAGAAGATGGTAGCATGTCAATAAAGAATGAAGAGGAAGAGCAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCGGTATCAATACCAATCACAGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCTGGAGTGTTGTGGGATGTCCCTTCACCCCCACCCGTGGGAAAGGCTGAACTGGAAGATGGAGCCTACAGAATCAAGCAAAAAGGGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCACACAATGTGGCACGTCACACGTGGCGCTGTCCTAATGCATAAAGGGAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGCTAGAAGGAGAATGGAAAGAAGGAGAAGAAGTCCAGGTCTTGGCATTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACAAAACCTGGCCTTTTCAAAACCAACACCGGAACCATAGGTGCCGTATCTCTGGACTTTTCCCCTGGAACGTCAGGATCTCCAATCGTCGACAAAAAAGGAAAAGTTGTGGGTCTCTATGGCAATGGTGTCGTTACAAGGAGTGGAGCATATGTGAGTGCCATAGCCCAGACTGAAAAAAGCATTGAAGACAATCCAGAGATTGAAGATGACATCTTTCGAAAGAAAAGATTGACCATCATGGACCTCCACCCAGGAGCGGGAAAGACAAAGAGATACCTCCCAGCCATAGTCAGAGAAGCCATAAAAAGAGGCTTGAGAACACTAATCCTGGCCCCCACTAGAGTCGTGGCAGCTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAAACCCCAGCCATCAGGGCTGAGCACACCGGGCGGGAGATTGTGGACCTAATGTGTCATGCCACATTTACCATGAGGCTGCTATCACCAATTAGGGTGCCAAATTACAACCTGATCATCATGGACGAAGCCCATTTCACAGACCCAGCAAGCATAGCAGCTAGAGGATACATCTCAACTCGAGTAGAGATGGGTGAAGCAGCTGGAATTTTTATGACAGCCACTCCTCCGGGTAGCAGAGACCCATTTCCTCAGAGCAATGCACCAATCATGGACGAAGAAAGAGAAATTCCTGAACGTTCGTGGAATTCCGGACATGAGTGGGTCACGGATTTTAAAGGGAAGACTGTTTGGTTTGTTCCAAGCATAAAAGCCGGAAATGACATAGCAGCCTGCCTGAGAAAAAATGGAAAGAGAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAATATGTCAAGACTAGAACCAATGACTGGGACTTCGTGGTCACAACTGACATCTCGGAAATGGGTGCCAACTTCAAAGCTGAGAGGGTTATAGACCCCAGACGCTGCATGAAACCAGTTATACTGACAGATGGTGAAGAGCGGGTGATCCTGGCAGGACCCATGCCAGTGACCCACTCTAGTGCAGCACAAAGAAGAGGGAGAATAGGAAGGAATCCAAAAAATGAAAATGACCAATACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAGGAAGCTAAGATGCTCCTAGATAACATCAACACACCTGAAGGAATCATTCCTAGCATGTTCGAGCCAGAGCGTGAAAAGGTGGATGCCATTGACGGTGAATACCGCTTGAGAGGAGAAGCAAGGAAAACCTTTGTGGACCTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCTTACAAAGTGGCAGCTGAAGGCATCAACTACGCAGACAGAAGGTGGTGTTTTGATGGAATCAGAAACAATCAAATCTTGGAAGAAAATGTGGAAGTGGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTAAAACCCAGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTCAAGGAATTTGCAGCCGGAAGAAAGTCCCTAACCCTGAACCTAATCACAGAGATGGGTAGGCTCCCAACTTTCATGACTCAGAAGGCAAGAGATGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAAGCAGGTGGAAGGGCATACAATCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTGCTGACACTTTTGGCCACAGTCACGGGAGGAATCTTTCTATTCTTGATGAGCGGAAGGGGTATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCCAGCATCCTCCTATGGTACGCACAAATACAGCCACATTGGATAGCAGCTTCAATAATACTGGAGTTCTTTCTCATAGTCTTGCTCATTCCAGAACCAGAAAAGCAGAGAACACCCCAGGATAACCAATTGACCTATGTTGTCATAGCCATCCTCACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTCCTGGAAAAAACAAAGAAAGACCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGCAACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACAACATTTATCACACCAATGTTGAGACATAGCATTGAAAATTCCTCAGTGAATGTGTCCCTAACAGCCATTGCCAACCAAGCCACAGTGCTAATGGGTCTTGGGAAAGGATGGCCATTGTCAAAGATGGACATCGGAGTTCCCCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATAACCCTCACAGCAGCTCTTCTTTTATTGGTAGCACATTATGCCATCATAGGACCAGGACTCCAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGCAGCAGCGGGCATCATGAAAAACCCAACTGTGGATGGAATAACAGTGATTGACCTAGATCCAATACCCTATGATCCAAAGTTTGAAAAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTGCTGATGATGAGGACTACGTGGGCTTTGTGTGAAGCCTTAACCCTAGCAACCGGGCCCATATCCACATTGTGGGAAGGAAATCCAGGGAGATTCTGGAACACAACCATTGCAGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCCATCATGAAGAACACAACCAGCACAAGAAGAGGAACTGGCAACATAGGAGAGACGCTAGGAGAGAAATGGAAAAGCCGACTGAACGCATTGGGGAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGACAGAACCTTAGCAAAAGAAGGCATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTCGAAAGAAATATGGTCACACCAGAAGGGAAAGTAGTGGACCTTGGTTGTGGCAGAGGGGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAACCCATCCCCATGTCAACATATGGGTGGAATCTAGTGCGTCTTCAGAGTGGAGTTGACGTTTTCTTCACTCCACCAGAGAAGTGTGACACATTGTTGTGTGACATAGGGGAGTCGTCACCAAATCCCACGGTAGAAGCAGGACGAACACTCAGAGTCCTTAACCTAGTGGAAAATTGGCTGAACAACAACACCCAATTTTGCATAAAGGTTCTCAACCCATACATGCCCTCAGTCATAGAAAAAATGGAAGCACTACAAAGGAAATATGGAGGAGCCTTGGTGAGAAATCCACTCTCACGGAATTCCACACATGAGATGTACTGGGTGTCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGGATGTTGATTAACAGATTCACAATGAGACACAAGAAAGCCACTTACGAGCCAGATGTTGACCTCGGAAGCGGAACCCGCAACATTGGAATTGAAAGTGAGACACCAAACCTAGACATAATTGGAAAAAGAATAGAAAAAATAAAACAAGAGCATGAAACGTCATGGCACTATGACCAAGACCACCCATACAAAACATGGGCTTACCATGGCAGCTATGAAACAAAACAGACTGGATCAGCATCATCCATGGTGAACGGAGTGGTCAGACTGCTGACAAAACCCTGGGACGTCGTTCCCATGGTGACACAGATGGCAATGACAGACACAACTCCTTTTGGACAACAGCGCGTTTTCAAAGAGAAAGTGGACACGAGAACCCAAGAACCAAAAGAAGGCACAAAAAAACTAATGAAAATCACGGCAGAGTGGCTTTGGAAAGAACTAGGAAAGAAAAAGACACCTAGGATGTGCACCAGAGAAGAATTCACAAAAAAGGTGAGAAGCAATGCAGCCTTGGGGGCCATATTCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATGGTAGGTTTTGGGAGCTGGTTGACAAGGAAAGGAATCTCCATCTTGAAGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAACTAGGAGAGTTTGGCAAAGCAAAAGGCAGCAGAGCCATATGGTACATGTGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTGAATGAAGACCATTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGCACAAGCTAGGTTACATCTTAAGAGACGTGAGCAAGAAAGAAGGAGGAGCAATGTATGCCGATGACACCGCAGGCTGGGACACAAGAATCACACTAGAGGACTTAAAAAATGAAGAAATGATAACAAACCACATGGAAGGAGAACACAAGAAACTTGCCGAGGCCATTTTCAAATTAACGTACCAAAACAAGGTGGTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGATATCATATCGAGAAGAGACCAAAGAGGTAGTGGACAAGTTGGCACCTATGGCCTCAATACTTTCACCAATATGGAAGCACAACTAATCAGGCAGATGGAGGGGGAAGGAATCTTCAAAAGCATCCAGCACTTGACAGCCACAGAAGAAATCGCTGTGCAAGATTGGCTAGCAAGAGTGGGGCGTGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTCTAGATGACAGGTTTGCAAGAGCTTTAACAGCTCTAAATGACATGGGAAAGGTTAGGAAAGACATACAACAATGGGAACCCTCAAGAGGATGGAACGATTGGACACAAGTGCCCTTCTGTTCACACCATTTCCATGAGTTAATCATGAAAGATGGTCGCACACTCGTAGTTCCATGTAGAAACCAAGATGAACTGATTGGTAGAGCCCGAATTTCCCAGGGAGCTGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCTTACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGTGATCTCAGGCTGGCGGCAAATGCCATTTGCTCGGCAGTCCCATCACATTGGGTTCCAACAAGCCGGACAACCTGGTCCATACACGCCAGCCATGAATGGATGACGACGGAAGACATGTTGACAGTCTGGAACAGGGTGTGGATCCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCATACCTGGGAAAAAGAGAAGACCAATGGTGCGGCTCACTGATTGGGCTAACAAGCAGGGCCACCTGGGCAAAGAACATCCAAACAGCAATAAATCAAGTCAGATCCCTCATTGGCAATGAGGAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAGGCAGGAGTCCTGTGGTAGAAGACAGAACTAACATGAAACAAGGCTAGAAGTCAGGTCGGATTAAGCCATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCACAAATGCCATAGCTTGAGCAAACTGTGCAGCCTGTAGCTCCACCTGAGAAGGTGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGTGAGATGAAGCTGTAGTCTCACTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/resources/denv3/genome_annotation.gff3 b/nextclade/resources/denv3/genome_annotation.gff3 index 709bb930..f0192507 100644 --- a/nextclade/resources/denv3/genome_annotation.gff3 +++ b/nextclade/resources/denv3/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_001475.2 1 10707 -NC_001475.2 feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; -NC_001475.2 feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; -NC_001475.2 feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; -NC_001475.2 feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; -NC_001475.2 feature gene 2414 3469 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_001475.2 feature gene 3470 4123 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_001475.2 feature gene 4124 4513 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_001475.2 feature gene 4514 6370 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_001475.2 feature gene 6371 6751 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_001475.2 feature gene 6752 6820 . + . codon_start=1;gene=2K;gene_name=2K; -NC_001475.2 feature gene 6821 7564 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_001475.2 feature gene 7565 10264 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome 1 10707 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 2414 3469 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 3470 4123 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 4124 4513 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 4514 6370 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 6371 6751 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 6752 6820 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 6821 7564 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome feature gene 7565 10264 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/resources/denv3/pathogen.json b/nextclade/resources/denv3/pathogen.json index aad0069c..1db88244 100644 --- a/nextclade/resources/denv3/pathogen.json +++ b/nextclade/resources/denv3/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/resources/denv3/reference.fasta b/nextclade/resources/denv3/reference.fasta index 8bf6921f..abe0db37 100644 --- a/nextclade/resources/denv3/reference.fasta +++ b/nextclade/resources/denv3/reference.fasta @@ -1,180 +1,2 @@ ->NC_001475.2 Dengue virus 3, complete genome -AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGACTCGGAAGCTTGCTTAACGTAG -TGCTGACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAGAAGACGGG -AAAACCGTCTATCAATATGCTGAAACGCGTGAGAAACCGTGTGTCAACTGGATCACAGTT -GGCGAAGAGATTCTCAAAAGGACTGCTGAACGGCCAGGGACCAATGAAATTGGTTATGGC -GTTCATAGCTTTCCTCAGATTTCTAGCCATTCCACCAACAGCAGGAGTCTTGGCTAGATG -GGGAACCTTCAAGAAGTCGGGGGCCATTAAGGTCCTGAAAGGCTTCAAGAAGGAGATCTC -AAACATGCTGAGCATAATCAACCAACGGAAAAAGACATCGCTCTGTCTCATGATGATATT -GCCAGCAGCACTTGCTTTCCACTTGACTTCACGAGATGGAGAGCCGCGCATGATTGTGGG -GAAGAATGAAAGAGGTAAATCCCTACTTTTTAAGACAGCCTCTGGAATCAACATGTGCAC -ACTCATAGCCATGGATTTGGGAGAGATGTGTGATGACACGGTCACTTACAAATGCCCCCA -CATTACCGAAGTGGAACCTGAAGACATTGACTGCTGGTGCAACCTTACATCAACATGGGT -GACTTATGGAACGTGCAATCAAGCTGGAGAGCATAGACGCGACAAGAGATCAGTGGCGTT -AGCTCCCCATGTCGGCATGGGACTGGACACACGCACCCAAACCTGGATGTCGGCTGAAGG -AGCTTGGAGACAAGTCGAGAAGGTAGAGACATGGGCCCTTAGGCACCCAGGGTTCACCAT -ACTAGCCCTATTTCTCGCCCATTACATAGGCACTTCCCTGACCCAGAAGGTGGTTATTTT -CATATTATTAATGCTGGTCACCCCATCCATGACAATGAGATGTGTGGGAGTAGGAAACAG -AGATTTTGTGGAAGGGCTATCAGGAGCTACGTGGGTTGACGTGGTGCTCGAGCACGGGGG -GTGTGTGACTACCATGGCTAAGAACAAGCCCACGCTGGATATAGAGCTTCAGAAGACCGA -GGCCACCCAACTGGCGACCCTAAGGAAGCTATGCATTGAGGGGAAAATTACCAACATAAC -AACTGACTCAAGATGTCCTACCCAAGGGGAAGCGGTTTTGCCTGAGGAGCAGGACCAGAA -CTACGTGTGTAAGCATACATACGTAGACAGAGGTTGGGGGAACGGTTGTGGTTTGTTTGG -CAAAGGAAGCTTGGTAACATGTGCGAAATTTCAATGCCTGGAACCAATAGAGGGAAAAGT -GGTGCAATATGAGAACCTCAAATACACCGTCATCATTACAGTGCACACAGGAGACCAACA -CCAGGTGGGAAATGAAACGCAAGGAGTCACGGCTGAGATAACACCTCAGGCATCAACCAC -TGAAGCCATCTTGCCTGAATATGGAACCCTTGGGCTAGAATGCTCACCACGGACAGGTTT -GGATTTCAATGAAATGATCTTACTAACAATGAAGAACAAAGCATGGATGGTACATAGACA -ATGGTTCTTTGACCTACCTCTACCATGGGCATCAGGAGCTACAACAGAAACACCAACCTG -GAACAGGAAGGAGCTTCTTGTGACATTCAAAAACGCACATGCGAAAAAACAAGAAGTAGT -TGTCCTTGGATCGCAAGAGGGAGCAATGCATACCGCACTGACAGGAGCTACAGAAATCCA -AAACTCAGGAGGCACAAGCATTTTCGCGGGGCACTTAAAATGTAGACTTAAGATGGACAA -ATTGGAACTCAAGGGGATGAGCTATGCAATGTGCACGAATACCTTTGTGTTGAAGAAAGA -AGTCTCAGAAACGCAGCACGGGACAATACTCATTAAGGTTGAGTACAAAGGGGAAGATGC -ACCTTGCAAGATTCCCTTTTCCACAGAGGATGGACAAGGGAAAGCTCATAATGGCAGACT -GATCACAGCCAACCCTGTGGTGACTAAGAAGGAGGAGCCTGTCAATATTGAGGCTGAACC -TCCTTTTGGGGAAAGCAATATAGTAATTGGAATTGGAGACAACGCCTTGAAAATCAACTG -GTACAAGAAGGGGAGCTCGATTGGGAAGATGTTCGAGGCCACTGAAAGGGGTGCAAGGCG -CATGGCCATCTTGGGAGACACAGCTTGGGACTTTGGATCAGTGGGTGGTGTTCTGAACTC -ATTAGGCAAAATGGTGCACCAAATATTTGGAAGTGCTTATACAGCCCTGTTCAGTGGAGT -CTCTTGGGTGATGAAAATTGGAATAGGTGTCCTCTTGACTTGGATAGGGTTGAATTCAAA -AAACACATCCATGTCATTTTCATGCATTGCGATAGGAATCATTACACTCTATCTGGGAGC -TGTGGTACAAGCTGACATGGGGTGTGTCATAAACTGGAAGGGCAAAGAACTCAAATGTGG -AAGCGGAATTTTCGTCACCAATGAGGTCCATACCTGGACAGAGCAATACAAATTCCAAGC -AGACTCCCCAAAAAGATTGGCAACAGCCATTGCAGGCGCCTGGGAGAATGGAGTGTGTGG -AATTAGGTCAACAACCAGAATGGAGAATCTCTTGTGGAAGCAAATAGCCAATGAACTGAA -CTACATATTATGGGAAAACAATATCAAATTAACGGTAGTTGTGGGCGATACACTTGGGGT -CTTAGAGCAAGGGAAAAGAACACTAACACCACAACCCATGGAGCTAAAATACTCATGGAA -AACGTGGGGAAAGGCAAAAATAGTGACAGCTGAAACACAAAATTCCTCTTTCATAATAGA -CGGGCCAAACACACCGGAGTGTCCAAGTGCCTCAAGAGCATGGAATGTGTGGGAGGTGGA -AGATTACGGGTTCGGAGTCTTCACAACCAACATATGGCTGAAACTCCGAGAGGTCTACAC -CCAACTATGTGACCATAGGCTAATGTCGGCAGCTGTCAAGGATGAGAGGGCCGTGCATGC -CGACATGGGCTACTGGATAGAAAGCCAAAAGAATGGAAGTTGGAAGCTAGAAAAAGCATC -CCTCATAGAGGTAAAAACCTGCACATGGCCAAAATCACACACTCTCTGGACTAATGGTGT -GCTAGAGAGTGACATGATCATCCCAAAGAGTCTAGCTGGTCCTATCTCACAACACAACTA -CAGGCCCGGGTACCACACCCAAACGGCAGGACCCTGGCACTTAGGAAAATTGGAGCTGGA -CTTCAACTACTGTGAAGGAACAACAGTTGTCATCACAGAAAGCTGTGGGACAAGAGGCCC -ATCATTGAGAACAACAACAGTGTCAGGGAAGTTGATACACGAATGGTGTTGCCGCTCGTG -CACACTTCCCCCCCTGCGATACATGGGAGAAGACGGCTGCTGGTATGGCATGGAAATCAG -ACCCATCAGTGAGAAAGAAGAGAACATGGTAAAGTCTTTAGTCTCAGCGGGAAGTGGAAA -GGTGGACAACTTCACAATGGGTGTCTTGTGTTTGGCAATCCTCTTTGAAGAGGTGTTGAG -AGGAAAATTTGGGAAGAAACACATGATTGCAGGGGTTTTCTTTACGTTTGTGCTCCTTCT -CTCAGGGCAAATAACATGGAGAGACATGGCGCACACACTAATAATGATCGGGTCCAACGC -CTCTGACAGGATGGGAATGGGCGTCACCTACCTAGCTCTAATTGCAACATTTAAAATCCA -GCCATTCTTGGCTTTGGGATTTTTCCTAAGAAAGCTGACATCTAGAGAAAATTTATTGTT -AGGAGTTGGGTTGGCCATGGCAACAACGTTACAACTGCCAGAGGACATTGAACAAATGGC -AAATGGAGTCGCTCTGGGGCTCATGGCTCTTAAACTGATAACACAATTTGAAACATACCA -ATTGTGGACGGCATTAGTCTCCTTAACGTGTTCAAACACAATTTTTACGTTGACTGTTGC -CTGGAGAACAGCCACTCTGATTTTGGCCGGAGTTTCGCTTTTACCAGTGTGCCAGTCTTC -AAGCATGAGGAAAACAGATTGGCTCCCAATGACAGTGGCAGCTATGGGAGTTCCACCCCT -TCCACTTTTTATTTTTAGCTTGAAAGACACACTCAAAAGGAGAAGCTGGCCACTGAATGA -AGGGGTGATGGCTGTTGGGCTTGTGAGCATTCTGGCCAGTTCTCTCCTTAGAAATGATGT -GCCCATGGCTGGACCATTAGTGGCCGGGGGCTTGCTGATAGCGTGCTACGTCATAACTGG -CACGTCAGCGGACCTCACTGTAGAAAAAGCCCCAGATGTAACATGGGAGGAAGAGGCTGA -GCAGACAGGAGTGTCCCACAACTTAATGATCACAGTTGATGATGATGGAACAATGAGAAT -AAAAGATGATGAGACTGAGAACATCCTAACAGTGCTTTTAAAAACAGCATTACTAATAGT -ATCAGGCATTTTTCCATACTCCATACCCGCAACATTGTTGGTCTGGCACACTTGGCAAAA -ACAAACCCAAAGATCCGGCGTTTTATGGGACGTACCCAGCCCCCCAGAGACACAGAAAGC -AGAACTGGAAGAAGGGGTTTATAGGATCAAACAGCAAGGAATTTTTGGGAAAACCCAAGT -AGGGGTTGGAGTACAGAAAGAAGGAGTCTTCCACACCATGTGGCACGTCACAAGAGGGGC -AGTGTTGACACATAATGGGAAAAGACTGGAACCAAACTGGGCTAGTGTGAAAAAAGATCT -GATTTCATATGGAGGAGGATGGAGACTGAGCGCACAATGGCAAAAGGGGGAGGAGGTGCA -GGTTATTGCCGTAGAGCCAGGGAAGAACCCAAAGAACTTTCAAACCACGCCAGGCACTTT -CCAGACTACTACAGGGGAAATAGGAGCAATTGCACTGGATTTCAAGCCTGGAACTTCAGG -ATCTCCTATCATAAATAGAGAGGGAAAGGTAGTGGGACTGTATGGCAATGGAGTGGTTAC -AAAGAATGGTGGCTATGTCAGCGGAATAGCGCAAACAAATGCAGAACCAGATGGACCGAC -ACCAGAGTTGGAAGAAGAGATGTTCAAAAAGCGAAACCTGACCATAATGGATCTTCATCC -TGGGTCAGGAAAGACACGGAAATACCTTCCAGCTATTGTCAGAGAGGCAATCAAGAGACG -TTTAAGAACCTTAATTTTGGCACCGACAAGGGTGGTTGCAGCTGAGATGGAAGAAGCATT -GAAAGGGCTCCCAATAAGGTACCAAACAACAGCAACAAAATCTGAACACACAGGAAGAGA -GATTGTTGATCTAATGTGCCACGCAACGTTCACAATGCGTTTGCTGTCACCAGTTAGGGT -TCCAAATTACAACTTGATAATAATGGATGAGGCCCATTTCACAGACCCAGCCAGTATAGC -GGCTAGAGGGTACATATCAACTCGTGTTGGAATGGGAGAGGCAGCCGCAATCTTCATGAC -AGCAACACCCCCTGGAACAGCTGATGCCTTTCCTCAGAGCAACGCTCCAATTCAAGATGA -AGAAAGGGACATACCAGAACGCTCATGGAATTCAGGCAATGAATGGATTACCGACTTCGC -TGGGAAAACGGTGTGGTTTGTCCCTAGCATTAAAGCCGGAAATGACATAGCAAACTGCTT -GCGAAAAAACGGGAAAAAAGTCATTCAACTTAGTAGGAAGACTTTTGACACAGAATATCA -GAAGACTAAACTGAATGATTGGGACTTTGTGGTGACAACTGACATTTCAGAAATGGGGGC -CAATTTCAAAGCAGATAGAGTGATCGACCCAAGAAGATGTCTCAAACCAGTGATCTTGAC -AGATGGACCAGAGCGGGTGATCCTGGCCGGACCAATGCCAGTCACCGCGGCGAGTGCTGC -GCAAAGGAGAGGGAGAGTTGGCAGGAACCCACAAAAAGAGAATGACCAGTACATATTCAC -GGGCCAGCCTCTCAACAATGATGAAGACCATGCTCACTGGACAGAAGCAAAAATGCTGCT -GGACAACATCAACACACCAGAAGGGATTATACCAGCTCTCTTTGAACCAGAAAGGGAGAA -GTCAGCCGCCATAGACGGTGAGTATCGCCTGAAGGGTGAGTCCAGGAAGACTTTCGTGGA -ACTCATGAGGAGGGGTGACCTTCCAGTTTGGTTAGCCCATAAAGTAGCATCAGAAGGAAT -CAAATACACAGATAGAAAATGGTGCTTTGATGGGCAACGCAATAATCAAATTTTAGAGGA -GAACATGGATGTGGAAATTTGGACAAAGGAAGGAGAAAAGAAAAAATTGAGACCTAGGTG -GCTTGATGCCCGCACTTATTCAGATCCATTGGCACTCAAGGAATTCAAGGACTTTGCGGC -TGGCAGAAAGTCAATCGCCCTTGATCTTGTGACAGAAATAGGAAGAGTGCCTTCACATCT -AGCCCACAGAACAAGAAACGCTCTGGACAATCTGGTGATGCTGCATACGTCAGAAGATGG -CGGTAGGGCTTACAGGCATGCGGTGGAGGAACTACCAGAAACAATGGAAACACTCCTACT -CTTGGGACTAATGATCTTGTTGACAGGTGGAGCAATGCTTTTCTTGATATCAGGTAAAGG -GATTGGAAAGACTTCAATAGGACTCATTTGTGTAATCGCTTCCAGCGGCATGTTGTGGAT -GGCCGAAGTTCCACTCCAATGGATCGCGTCGGCTATAGTCCTGGAGTTTTTTATGATGGT -GTTGCTCATACCAGAACCAGAAAAGCAGAGAACCCCCCAAGACAACCAACTCGCATATGT -CGTGATAGGCATACTTACATTGGCTGCAACAATAGCAGCCAATGAAATGGGACTGCTGGA -AACCACAAAGAGAGACTTAGGAATGTCTAAGGAGCCAGGTGTTGTTTCTCCAACCAGCTA -TTTGGATGTGGACTTGCACCCAGCATCAGCCTGGACATTGTACGCCGTGGCCACTACAGT -AATAACACCAATGTTAAGACATACCATAGAGAATTCTACAGCAAATGTGTCCCTGGCAGC -TATAGCCAACCAGGCAGTGGTCCTGATGGGTTTGGACAAAGGATGGCCAATATCAAAAAT -GGACTTAGGCGTGCCACTACTGGCACTGGGTTGCTATTCACAAGTGAACCCACTGACTCT -AACTGCGGCAGTACTTTTGCTAATCACACATTATGCTATCATAGGTCCAGGATTGCAAGC -AAAAGCCACCCGTGAAGCTCAGAAAAGGACAGCTGCTGGAATAATGAAGAATCCAACAGT -GGATGGGATAATGACAATAGACCTAGATTCTGTAATATTTGATTCAAAATTTGAAAAACA -ACTGGGACAGGTTATGCTCCTGGTTTTGTGCGCAGTCCAACTCTTGCTAATGAGAACATC -ATGGGCCTTGTGTGAAGCTTTAACTCTAGCTACAGGACCAATAACAACACTCTGGGAAGG -ATCACCTGGTAAGTTCTGGAACACCACGATAGCTGTTTCCATGGCGAACATTTTTAGAGG -GAGCTATTTAGCAGGAGCTGGGCTTGCTTTTTCTATTATGAAATCAGTTGGAACAGGAAA -AAGAGGAACAGGCTCACAAGGTGAAACTTTAGGAGAAAAATGGAAAAAGAAATTAAATCA -ATTATCCCGGAAAGAGTTTGACCTTTACAAGAAATCTGGAATCACTGAAGTGGATAGAAC -AGAAGCCAAAGAAGGGTTGAAAAGAGGAGAGACAACACATCATGCCGTGTCCCGAGGTAG -CGCAAAACTTCAATGGTTTGTGGAAAGAAACATGGTCGTTCCCGAAGGAAGAGTCATAGA -CTTGGGCTGTGGAAGAGGAGGCTGGTCATATTACTGTGCAGGACTGAAAAAAGTCACAGA -AGTGCGAGGATACACAAAAGGCGGTCCAGGACACGAAGAACCAGTACCTATGTCTACATA -TGGATGGAACATAGTTAAGTTAATGAGCGGAAAGGATGTGTTCTATCTCCCACCTGAAAA -GTGTGATACCCTGTTGTGTGACATTGGAGAATCTTCACCAAGCCCAACAGTGGAAGAGAG -CAGAACTATAAGAGTTTTGAAGATGGTTGAACCATGGCTAAAAAACAACCAGTTTTGCAT -TAAAGTTTTGAACCCTTACATGCCAACTGTGATTGAGCACCTAGAAAGACTACAAAGGAA -ACATGGAGGAATGCTTGTGAGAAATCCACTTTCACGAAACTCCACGCACGAAATGTACTG -GATATCTAATGGCACAGGTAACATTGTCTCTTCAGTCAACATGGTGTCTAGATTGCTACT -GAACAGGTTCACGATGACACACAGGAGACCCACCATAGAGAAAGATGTGGATTTAGGAGC -AGGAACTCGACATGTTAATGCGGAACCAGAAACACCCAACATGGATGTCATTGGGGAAAG -AATAAAAAGGATCAAGGAGGAGCATAATTCAACATGGCACTATGATGACGAAAACCCCTA -CAAAACGTGGGCTTACCATGGATCCTATGAAGTCAAAGCCACAGGCTCAGCCTCCTCCAT -GATAAATGGAGTCGTGAAACTCCTCACCAAACCATGGGATGTGGTGCCCATGGTGACACA -GATGGCAATGACAGACACAACTCCATTTGGCCAGCAGAGAGTCTTTAAAGAGAAAGTGGA -CACCAGGACGCCCAGGCCCATGCCAGGGACAAGAAAGGCTATGGAGATCACAGCGGAGTG -GCTCTGGAGAACCCTGGGAAGGAACAAAAGACCCAGATTATGCACAAGGGAAGAGTTTAC -AAAAAAGGTCAGAACTAACGCAGCCATGGGCGCCGTTTTCACAGAGGAGAACCAATGGGA -CAGTGCGAAAGCTGCTGTTGAGGATGAAGAATTTTGGAAACTTGTGGACAGAGAACGTGA -ACTCCACAAATTGGGCAAATGTGGAAGCTGCGTTTATAACATGATGGGCAAGAGAGAGAA -AAAACTTGGAGAGTTTGGCAAAGCAAAAGGCAGTAGAGCTATATGGTACATGTGGTTGGG -AGCCAGGTACCTTGAGTTCGAAGCCCTTGGATTCTTAAATGAAGACCACTGGTTCTCGCG -TGAAAACTCTTACAGTGGAGTAGAAGGAGAAGGACTGCACAAGCTAGGCTACATATTAAG -GGACATTTCCAAGATACCCGGAGGAGCCATGTATGCTGATGACACAGCTGGTTGGGACAC -AAGAATAACAGAAGATGACCTGCACAATGAGGAAAAGATCATACAGCAAATGGACCCTGA -ACACAGGCAGTTAGCGAACGCTATATTCAAGCTCACATACCAAAACAAAGTGGTCAAAGT -TCAACGACCGACTCCAACGGGCACGGTAATGGATATTATATCTAGGAAAGACCAAAGGGG -CAGTGGACAACTGGGAACTTATGGCCTGAATACATTCACCAACATGGAAGCCCAGTTAGT -CAGACAAATGGAAGGAGAAGGTGTGCTGACAAAGGCAGACCTCGAGAACCCTCATCTGCT -AGAGAAGAAAATCACACAATGGTTGGAAACCAAAGGAGTGGAGAGGTTAAAAAGAATGGC -CATTAGCGGGGATGATTGCGTGGTGAAACCAATCGATGACAGGTTCGCTAATGCCCTGCT -TGCTTTGAACGATATGGGAAAGGTTCGGAAAGACATACCTCAATGGCAGCCATCAAAGGG -ATGGCATGATTGGCAACAGGTTCCTTTCTGCTCCCACCACTTTCATGAATTGATCATGAA -AGATGGAAGAAAGTTGGTGGTTCCCTGCAGACCCCAGGACGAACTAATAGGAAGAGCAAG -AATCTCTCAAGGAGCGGGATGGAGCCTTAGAGAAACTGCATGTCTGGGGAAAGCCTACGC -CCAAATGTGGAGTCTCATGTATTTTCACAGAAGAGATCTCAGATTAGCATCCAACGCCAT -ATGTTCAGCAGTACCAGTCCACTGGGTTCCCACAAGTAGAACGACATGGTCTATTCATGC -TCACCATCAGTGGATGACTACAGAAGACATGCTTACTGTTTGGAACAGGGTGTGGATAGA -GGAAAATCCATGGATGGAAGACAAAACTCCAGTTACAACTTGGGAAAATGTTCCATATCT -AGGAAAGAGAGAAGACCAATGGTGTGGATCACTTATTGGTCTCACTTCCAGAGCAACCTG -GGCCCAGAACATACCCACAGCAATTCAACAGGTGAGAAGCCTTATAGGCAATGAAGAGTT -CCTGGACTACATGCCTTCAATGAAGAGATTCAGGAAGGAAGAGGAGTCGGAGGGAGCCAT -TTGGTAAACGTAGGAAGTGGAAAAGAGGCTAACTGTCAGGCCACCTTAAGCCACAGTACG -GAAGAAGCTGTGCTGCCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGAAGTCAGGCCCC -AAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGTCGTGGGGACGTAAAACCTG -GGAGGCTGCAAACTGTGGAAGCTGTACGCACGGTGTAGCAGACTAGCGGTTAGAGGAGAC -CCCTCCCATGACACAACGCAGCAGCGGGGCCCGAGCACTGAGGGAAGCTGTACCTCCTTG -CAAAGGACTAGAGGTTAGAGGAGACCCCCCGCAAATAAAAACAGCATATTGACGCTGGGA -GAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGG -AATGGTGCTGTTGAATCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome +AGTTGTTAGTCTACGTGGACCGACAAGAACAGTTTCGACTCGGAAGCTTGCTTAACGTAGTGCTGACAGTTTTTTATTAGAGAGCAGATCTCTGATGAACAACCAACGGAAAAAGACGGGAAAACCGTCTATCAATATGCTGAAACGCGTGAGAAACCGTGTGTCAACTGGATCACAGTTGGCGAAGAGATTCTCAAGAGGATTGCTGAACGGCCAAGGACCAATGAAATTGGTTATGGCGTTCATAGCTTTCCTCAGATTTCTAGCCATTCCACCGACAGCAGGAGTCTTGGCTAGATGGGGTACCTTCAAGAAGTCGGGGGCTATTAAGGTCCTAAAAGGCTTCAAGAAGGAGATCTCAAACATGCTGAGCATTATCAACAAACGGAAAAAGACATCGCTCTGTCTCATGATGATGTTACCAGCAACACTTGCTTTCCACTTGACTTCACGAGATGGAGAGCCGCGCATGATTGTGGGGAAGAATGAAAGAGGAAAATCCCTACTTTTTAAGACAGCCTCTGGAATCAACATGTGCACACTCATAGCCATGGATTTGGGAGAGATGTGTGATGACACGGTCACTTACAAATGCCCCCACATTACCGAAGTGGAGCCTGAAGACATTGACTGCTGGTGCAACCTTACATCGACATGGGTGACTTATGGAACGTGCAATCAAGCTGGAGAGCATAGACGCGATAAGAGATCAGTGGCGTTAGCTCCCCATGTCGGCATGGGACTGGACACACGCACCCAAACCTGGATGTCGGCTGAAGGAGCTTGGAGACAAGTCGAGAAGGTAGAGACATGGGCCCTTAGGCACCCAGGGTTCACCATACTAGCCCTATTTCTTGCCCATTACATAGGCACTTCCTTGACCCAGAAAGTGGTTATTTTTATACTACTAATGCTGGTCACCCCATCCATGACAATGAGATGTGTGGGAGTAGGAAACAGAGATTTTGTGGAAGGCCTATCGGGAGCTACGTGGGTTGACGTGGTGCTCGAGCACGGTGGGTGTGTGACTACCATGGCTAAGAACAAGCCCACGCTGGATATAGAGCTTCAGAAGACCGAGGCCACCCAACTGGCGACCCTAAGGAAGCTATGCATTGAGGGAAAAATTACCAACATAACAACCGACTCAAGGTGTCCCACCCAAGGGGAAGCGATTTTACCTGAGGAGCAGGACCAGAACTACGTGTGTAAGCATACATACGTGGACAGAGGCTGGGGAAACGGTTGTGGTTTGTTTGGCAAGGGAAGCTTGGTGACATGCGCGAAATTTCAATGTTTAGAATCAATAGAGGGAAAAGTGGTGCAACATGAGAACCTCAAATACACCGTCATCATCACAGTGCACACAGGAGACCAACACCAGGTGGGAAATGAAACGCAGGGAGTCACGGCTGAGATAACACCCCAGGCATCAACCGCTGAAGCCATCTTACCTGAATATGGAACCCTTGGGCTAGAATGCTCACCACGGACAGGTTTGGATTTCAATGAAATGATCTTATTGACAATGAAGAACAAAGCATGGATGGTACATAGACAATGGTTCTTTGACCTACCTCTACCATGGACATCAGGAGCTACAACAGAAACACCAACCTGGAACAGGAAAGAGCTTCTTGTGACATTCAAAAACGCACATGCAAAAAAACAAGAAGTAGTTGTCCTTGGATCGCAAGAGGGAGCAATGCATACAGCACTGACAGGAGCTACAGAGATCCAAACCTCAGGAGGCACAAGCATTTTTGCGGGGCACTTAAAATGTAGACTCAAGATGGACAAATTGGAACTCAAGGGGATGAGCTATGCAATGTGCTTGAATACCTTTGTGTTGAAGAAAGAAGTCTCCGAAACGCAGCATGGGACAATACTCATTAAGGTTGAGTACAAAGGGGAAGATGCACCCTGCAAGATTCCTTTCTCCACGGAGGATGGACAAGGGAAAGCTCACAATGGCAGACTGATCACAGCCAACCCAGTGGTGACCAAGAAGGAGGAGCCTGTCAATATTGAGGCTGAACCTCCTTTTGGGGAAAGTAATATAGTAATTGGAATTGGAGACAAAGCCTTGAAAATCAACTGGTACAAGAAGGGAAGCTCGATTGGGAAGATGTTCGAGGCCACTGCCAGAGGTGCAAGGCGCATGGCCATCTTGGGAGACACAGCCTGGGACTTTGGATCAGTGGGTGGTGTTTTGAATTCATTAGGGAAAATGGTGCACCAAATATTTGGAAGTGCTTACACAGCCCTATTTAGTGGAGTCTCCTGGATAATGAAAATTGGAATAGGTGTCCTCTTAACCTGGATAGGGTTGAATTCAAAAAACACTTCTATGTCATTTTCATGCATTGCGATAGGAATCATTACACTCTATCTGGGAGCCGTGGTGCAAGCTGACATGGGGTGTGTCATAAACTGGAAAGGCAAAGAACTCAAATGTGGAAGTGGAATTTTCGTCACTAATGAGGTCCACACCTGGACAGAGCAATACAAATTTCAAGCAGACTCCCCCAAAAGACTGGCGACAGCCATTGCAGGCGCTTGGGAGAATGGAGTGTGCGGAATCAGGTCAACAACCAGAATGGAGAACCTCTTGTGGAAGCAAATAGCCAATGAACTGAACTACATATTATGGGAAAACAACATCAAATTAACGGTAGTTGTGGGCGACATAATTGGGGTCTTAGAGCAAGGGAAAAGAACACTAACACCACAACCCATGGAGCTAAAATATTCATGGAAAACATGGGGAAAGGCAAAAATAGTGACAGCTGAAACACAAAATTCCTCTTTCATAATAGATGGGCCAAACACACCGGAGTGTCCAAGTGCCTCAAGAGCATGGAATGTGTGGGAGGTGGAAGATTACGGGTTCGGAGTCTTCACAACCAACATATGGCTGAAACTCCGAGAGGTGTACACCCAACTATGTGACCATAGGCTAATGTCGGCAGCCGTCAAGGATGAGAGGGCCGTACACGCCGACATGGGCTATTGGATAGAAAGCCAAAAGAATGGAAGTTGGAAGCTAGAAAAAGCATCCCTCATAGAGGTGAAAACCTGCACATGGCCAAAATCACACACTCTTTGGAGCAATGGTGTGCTAGAGAGTGACATGATCATCCCAAAGAGTCTAGCTGGTCCTATTTCGCAACACAACCACAGGCCCGGGTACCACACCCAAACGGCAGGACCCTGGCACTTAGGAAAATTGGAGCTGGACTTCAACTATTGTGAAGGAACAACAGTTGTCATCACAGAAAACTGTGGGACAAGAGGCCCATCATTGAGAACAACAACAGTGTCAGGGAAGTTGATACACGAATGGTGTTGCCGCTCGTGCACACTTCCTCCCCTGCGATACATGGGAGAAGACGGCTGCTGGTATGGCATGGAAATTAGACCCATTAATGAGAAAGAAGAGAACATGGTAAAGTCTTTAGCCTCAGCAGGGAGTGGAAAGGTGGACAACTTCACAATGGGTGTCTTGTGTTTGGCAATCCTCTTTGAAGAGGTGATGAGAGGAAAATTTGGGAAAAAACACATGATTGCAGGGGTTCTCTTCACGTTTGTGCTCCTTCTCTCAGGGCAAATAACATGGAGAGACATGGCGCACACACTCATAATGATTGGGTCCAACGCCTCTGACAGAATGGGAATGGGCGTCACTTACCTAGCTTTAATTGCAACATTTAAAATTCAGCCATTCTTGGCTTTGGGATTCTTCCTGAGGAAACTGACATCTAGAGAAAATTTATTGTTGGGAGTTGGGTTGGCCATGGCAACAACGTTACAACTGCCAGAGGACATTGAACAAATGGCGAATGGAATTGCTTTGGGGCTCATGGCTCTTAAACTGATAACACAATTTGAAACATACCAACTATGGACGGCATTAGTCTCCCTAACGTGTTCAAATACAATTTTCACGTTGACTGTTGCCTGGAGAACAGCCACCCTGATTTTGGCCGGAATTTCGCTTTTGCCAGTGTGCCAGTCTTCGAGCATGAGGAAAACAGATTGGCTCCCAATGACTGTGGCAGCTATGGGAGTTCCACCCCTACCACTTTTTATCTTCAGTTTGAAAGATACACTCAAAAGGAGAAGCTGGCCACTGAATGAGGGGGTGATGGCTGTTGGACTTGTGAGCATTCTAGCTAGTTCTCTCCTTAGGAATGATGTGCCCATGGCTGGACCATTAGTGGCTGGGGGCTTGCTGATAGCGTGCTACGTCATAACTGGCACGTCAGCAGACCTCACTGTAGAAAAAGCAGCAGATGTAACATGGGAGGAAGAGGCTGAGCAAACAGGAGTGTCCCACAATTTAATGATCACAGTTGATGATGATGGAACAATGAGAATAAAAGATGATGAGACTGAGAACATCCTAACAGTGCTTTTAAAAACAGCATTACTAATAGTATCAGGCATCTTTCCATACTCCATACCCGCAACACTGTTGGTCTGGCATACTTGGCAAAAGCAAACCCAAAGATCCGGCGTCCTATGGGACGTACCCAGCCCCCCAGAGACACAGAAAGCAGAACTGGAAGAAGGGGTCTATAGGATCAAACAGCAAGGAATTTTTGGGAAAACCCAAGTGGGGGTTGGAGTACAGAAAGAAGGAGTTTTCCACACCATGTGGCACGTCACAAGAGGGGCAGTGTTGACACACAATGGGAAAAGACTGGAACCAAACTGGGCTAGCGTGAAAAAAGATCTGATTTCATACGGAGGAGGATGGAGATTGAGTGCACAATGGCAAAAGGGAGAGGAGGTGCAGGTTATTGCCGTAGAGCCTGGGAAGAACCCAAAGAACTTTCAAACCATGCCAGGCATTTTTCAGACAACAACAGGGGAAATAGGAGCAATTGCACTGGACTTCAAGCCTGGAACTTCAGGATCTCCCATCATAAACAGAGAGGGAAAGGTAGTGGGACTGTATGGCAATGGAGTGGTTACAAAGAATGGTGGCTATGTCAGTGGAATAGCGCAAACAAATGCAGAACCAGACGGACCGACACCAGAGTTGGAAGAAGAGATGTTCAAAAAGCGAAATCTAACCATAATGGATCTTCATCCTGGGTCAGGAAAGACGCGGAAATACCTTCCAGCTATTGTTAGAGAGGCAATCAAGAGACGCTTAAGGACTCTAATTTTGGCACCAACAAGGGTGGTTGCAGCTGAGATGGAAGAAGCATTGAAAGGGCTCCCAATAAGGTATCAAACAACTGCAACAAAATCTGAACACACAGGAAGAGAGATTGTTGATCTAATGTGCCACGCAACGTTCACAATGCGCTTGCTGTCACCAGTCAGGGTTCCAAACTACAACTTGATAATAATGGATGAGGCTCATTTCACAGACCCAGCCAGTATAGCGGCTAGAGGGTACATATCAACTCGTGTAGGAATGGGAGAGGCAGCCGCAATTTTCATGACAGCAACACCCCCTGGAACAGCTGATGCCTTTCCTCAGAGCAACGCTCCAATTCAAGATGAAGAAAGGGACATACCGGAACGCTCATGGAATTCAGGCAATGAATGGATTACCGACTTTGTTGGGAAGACGGTGTGGTTTGTCCCTAGCATCAAAGCCGGAAATGACATAGCAAACTGCTTGCGGAAAAACGGAAAAAAGGTCATTCAACTTAGTAGGAAGACTTTTGACACAGAATATCAAAAGACTAAACTGAATGATTGGGACTTTGTGGTGACAACAGACATTTCAGAAATGGGAGCCAATTTCAAAGCAGATAGAGTGATCGACCCAAGAAGATGTCTCAAGCCAGTGATTTTGACAGATGGACCCGAGCGGGTGATCCTGGCTGGACCAATGCCAGTCACCGTAGCGAGCGCTGCGCAAAGGAGAGGGAGAGTTGGCAGGAACCCACAAAAAGAAAATGACCAGTACATATTCACGGGCCAGCCTCTCAACAATGATGAAGACCATGCTCACTGGACAGAAGCAAAAATGCTGCTGGACAACATCAACACACCAGAAGGGATTATACCAGCTCTCTTTGAACCAGAAAGGGAGAAGTCAGCCGCCATAGACGGCGAATACCGCCTGAAGGGTGAGTCCAGGAAGACCTTCGTGGAACTCATGAGGAGGGGTGACCTCCCAGTTTGGCTAGCCCATAAAGTAGCATCAGAAGGGATCAAATATACAGATAGAAAATGGTGCTTTGATGGAGAACGTAATAATCAAATTTTAGAGGAGAATATGGATGTGGAAATCTGGACAAAGGAAGGAGAAAAGAAAAAATTGAGACCTAGGTGGCTTGATGCCCGCACTTATTCAGATCCCTTAGCACTCAAGGAATTCAAGGATTTTGCAGCTGGCAGAAAGTCAATCGCCCTTGATCTTGTGACAGAAATAGGAAGAGTGCCTTCACACTTAGCCCACAGAACGAGAAACGCCCTGGACAATTTGGTGATGCTGCACACGTCAGAACATGGCGGTAGGGCCTACAGGCATGCAGTGGAGGAACTACCAGAAACAATGGAAACACTCTTACTCCTGGGACTCATGATCTTGTTAACAGGTGGAGCAATGCTTTTCTTGATATCAGGTAAAGGGATTGGAAAGACTTCAATAGGACTCATTTGTGTAATTGCTTCCAGCGGCATGTTATGGATGGCTGATGTCCCACTCCAATGGATCGCGTCGGCTATAGTCCTGGAGTTTTTTATGATGGTGTTGCTCATACCAGAACCAGAAAAGCAGAGAACTCCCCAAGACAACCAACTCGCATATGTCGTGATAGGCATACTTACATTGGCTGCAATAGTAGCAGCCAATGAAATGGGACTGTTGGAAACTACAAAGAGAGATTTAGGAATGTCTAAAGAACCAGGTGTTGTTTCTCCAACCAGCTATTTGGATGTGGACTTGCACCCAGCATCAGCCTGGACATTGTACGCCGTGGCCACAACAGTAATAACACCAATGTTGAGACATACCATAGAGAATTCCACAGCAAATGTGTCCCTGGCAGCTATAGCTAACCAGGCAGTGGTCCTGATGGGTTTAGACAAAGGATGGCCGATATCGAAAATGGACTTAGGCGTACCACTACTGGCACTGGGTTGCTATTCACAAGTGAACCCACTAACTCTCACAGCGGCAGTACTTTTGCTAGTCACACATTATGCTATTATAGGTCCAGGATTGCAGGCAAAAGCCACTCGTGAAGCTCAGAAAAGGACAGCTGCTGGAATAATGAAGAATCCAACGGTGGATGGGATAATGACAATAGACCTAGATCCTGTAATATACGATTCAAAATTTGAAAAGCAACTAGGACAGGTTATGCTCCTGGTTCTGTGTGCAGTTCAACTTTTGTTAATGAGAACATCATGGGCCTTGTGTGAAGCTCTAACCCTAGCCACAGGACCAATAACAACACTCTGGGAAGGATCACCTGGGAAGTTTTGGAACACCACGATAGCTGTTTCCATGGCGAACATCTTTAGAGGGAGCTATTTAGCAGGAGCTGGGCTTGCTTTTTCTATCATGAAATCAGTTGGAACAGGAAAGAGAGGAACAGGGTCACAAGGTGAAACCTTAGGAGAAAAGTGGAAAAAGAAATTAAATCAGTTATCCCGGAAAGAGTTTGACCTTTACAAGAAATCCGGAATCACTGAAGTGGATAGAACAGAAGCCAAAGAAGGGTTGAAAAGAGGAGAAATAACACACCATGCCGTGTCCAGAGGCAGCGCAAAACTTCAATGGTTCGTGGAGAGAAACATGGTCATTCCCGAAGGAAGAGTCATAGACTTAGGCTGTGGAAGAGGAGGCTGGTCATATTACTGTGCAGGACTGAAAAAAGTTACAGAAGTGCGAGGATACACAAAAGGCGGCCCAGGACACGAAGAACCAGTACCTATGTCTACATACGGATGGAACATAGTCAAGTTAATGAGTGGAAAGGATGTGTTTTATCTTCCACCTGAAAAGTGTGATACCCTATTGTGTGACATTGGAGAATCTTCACCAAGCCCAACAGTGGAAGAAAGCAGAACCATAAGAGTCTTGAAGATGGTTGAACCATGGCTAAAAAACAACCAGTTTTGCATTAAAGTATTGAACCCTTACATGCCAACTGTGATTGAGCACCTAGAAAGACTACAAAGGAAACATGGAGGAATGCTTGTGAGAAATCCACTCTCACGAAACTCCACGCACGAAATGTACTGGATATCCAATGGTACAGGCAACATCGTCTCTTCAGTCAACATGGTATCCAGATTGCTACTGAACAGATTCACAATGACACACAGGAGACCCACCATAGAGAAAGATGTGGATTTAGGAGCAGGAACCCGACATGTCAATGCGGAACCAGAAACACCCAACATGGATGTCATTGGGGAAAGAATAAAAAGGATCAAGGAGGAGCATAGTTCAACATGGCACTATGATGATGAAAATCCTTACAAAACGTGGGCTTACCATGGATCCTATGAAGTCAAAGCCACAGGCTCAGCCTCCTCCATGATAAATGGAGTCGTGAAACTCCTCACAAAACCATGGGATGTGGTGCCCATGGTGACACAGATGGCAATGACAGATACAACCCCATTTGGCCAGCAAAGAGTTTTTAAAGAGAAAGTGGACACCAGGACACCCAGGCCCATGCCAGGAACAAGAAAGGTTATGGAGATCACAGCGGAGTGGCTTTGGAGAACCCTGGGAAGGAACAAAAGACCCAGATTATGCACAAGGGAGGAGTTCACAAAAAAGGTCAGAACCAACGCAGCTATGGGCGCCGTTTTCACAGAGGAGAACCAATGGGACAGTGCGAGAGCTGCTGTTGAGGACGAAGAATTTTGGAAACTTGTGGACAGAGAACGTGAACTCCACAAATTGGGCAAGTGTGGAAGCTGCGTTTACAACATGATGGGCAAGAGAGAGAAGAAACTTGGAGAGTTTGGCAAAGCAAAAGGCAGTAGAGCTATATGGTACATGTGGTTGGGAGCCAGGTACCTTGAGTTCGAGGCACTCGGATTCTTAAATGAAGACCACTGGTTCTCGCGTGAAAACTCTTACAGTGGAGTAGAAGGAGAAGGACTGCACAAGCTGGGATACATCTTAAGAGATATTTCCAAGATACCCGGAGGAGCTATGTATGCTGATGACACAGCTGGTTGGGACACAAGAATAACAGAAGATGACCTGCACAATGAGGAAAAAATCACACAGCAAATGGACCCTGAACACAGGCAGTTAGCGAACGCTATATTCAAGCTCACATACCAAAACAAAGTGGTCAAAGTTCAACGACCAACTCCAAAGGGCACGGTAATGGACATCATATCTAGGAAAGACCAAAGAGGCAGTGGACAGGTGGGAACTTATGGTCTGAATACATTCACCAACATGGAAGCCCAGTTAATCAGACAAATGGAAGGAGAAGGTGTGTTGTCAAAGGCAGACCTCGAGAACCCTCATCTGCTAGAGAAGAAAATTACACAATGGTTGGAAACCAAAGGAGTGGAGAGGTTAAAAAGAATGGCCATCAGCGGGGATGATTGCGTAGTGAAACCAATCGATGACAGGTTCGCCAATGCCCTGCTTGCCCTGAACGATATGGGAAAGGTTAGGAAGGACATACCTCAATGGCAGCCATCAAAGGGATGGCATGATTGGCAACAGGTCCCTTTCTGCTCCCACCACTTTCATGAATTGATCATGAAAGATGGAAGAAAGTTGGTAGTTCCCTGCAGACCCCAGGACGAACTAATAGGAAGAGCGAGAATCTCTCAAGGAGCAGGATGGAGCCTTAGAGAAACTGCATGTCTAGGGAAAGCCTACGCTCAAATGTGGACTCTCATGTATTTTCACAGAAGAGATCTTAGACTAGCATCCAACGCCATATGTTCAGCAGTACCAGTCCATTGGGTCCCCACAAGCAGAACGACATGGTCTATTCATGCTCACCATCAGTGGATGACTACAGAAGACATGCTTACTGTCTGGAACAGGGTGTGGATAGAGGACAATCCATGGATGGAAGACAAAACTCCAGTCACAACTTGGGAAGATGTTCCATATCTAGGGAAGAGAGAAGACCAATGGTGCGGATCACTCATTGGTCTCACTTCCAGAGCAACCTGGGCCCAGAACATACTCACAGCAATCCAACAGGTGAGAAGCCTTATAGGCAATGAAGAGTTTCTGGACTACATGCCTTCGATGAAGAGATTCAGGAAGGAGGAGGAGTCAGAGGGAGCCATTTGGTAAACGCAGGAAGTGAAAAAGAGGCAAACTGTCAGGCCACCTTAAGCCACAGTACGGAAGAAGCTGTGCAGCCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGAAGTCAGGCCCAAAAGCCACGGTTTGAGCAAACCGTGCTGCCTGTAGCTCCGTCGTGGGGACGTAAAGCCTGGGAGGCTGCAAACCGTGGAAGCTGTACGCACGGTGTAGCAGACTAGCGGTTAGAGGAGACCCCTCCCATGACACAACGCAGCAGCGGGGCCCGAGCACTGAGGGAAGCTGTACCTCCTTGCAAAGGACTAGAGGTTAGAGGAGACCCCCCGCAAATAAAAACAGCATATTGACGCTGGGAGAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT diff --git a/nextclade/resources/denv4/genome_annotation.gff3 b/nextclade/resources/denv4/genome_annotation.gff3 index a417d706..0b573bda 100644 --- a/nextclade/resources/denv4/genome_annotation.gff3 +++ b/nextclade/resources/denv4/genome_annotation.gff3 @@ -1,14 +1,14 @@ ##gff-version 3 -##sequence-region NC_002640.1 1 10649 -NC_002640.1 feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; -NC_002640.1 feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; -NC_002640.1 feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; -NC_002640.1 feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; -NC_002640.1 feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; -NC_002640.1 feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; -NC_002640.1 feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; -NC_002640.1 feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; -NC_002640.1 feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; -NC_002640.1 feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; -NC_002640.1 feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; -NC_002640.1 feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file +##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome 1 10649 +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; +Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; \ No newline at end of file diff --git a/nextclade/resources/denv4/pathogen.json b/nextclade/resources/denv4/pathogen.json index ee6e6797..d5ce36c8 100644 --- a/nextclade/resources/denv4/pathogen.json +++ b/nextclade/resources/denv4/pathogen.json @@ -1,5 +1,9 @@ { "alignmentParams": { + "penaltyGapOpen": 8, + "penaltyGapOpenInFrame": 12, + "penaltyGapOpenOutOfFrame": 14, + "gapAlignmentSide": "left", "minSeedCover": 0.1, "minLength": 1000 }, @@ -17,6 +21,7 @@ "experimental": true, "files": { "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", "genomeAnnotation": "genome_annotation.gff3", "pathogenJson": "pathogen.json", "readme": "README.md", @@ -29,7 +34,7 @@ }, "qc": { "frameShifts": { - "enabled": false + "enabled": true }, "missingData": { "enabled": false, @@ -55,7 +60,7 @@ "windowSize": 100 }, "stopCodons": { - "enabled": false + "enabled": true } }, "schemaVersion": "3.0.0", diff --git a/nextclade/resources/denv4/reference.fasta b/nextclade/resources/denv4/reference.fasta index 1abd4ccc..a6b134fc 100644 --- a/nextclade/resources/denv4/reference.fasta +++ b/nextclade/resources/denv4/reference.fasta @@ -1,179 +1,2 @@ ->NC_002640.1 Dengue virus 4, complete genome -AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAG -TTCTAACAGTTTGTTTGAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGG -TGGTTAGACCACCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAG -GGTTGGTGAAGAGATTCTCAACCGGACTTTTTTCTGGGAAAGGACCCTTACGGATGGTGC -TAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAGA -GATGGGGACAGTTGAAGAAAAATAAGGCCATCAAGATACTGATTGGATTCAGGAAGGAGA -TAGGCCGCATGCTGAACATCTTGAACGGGAGAAAAAGGTCAACGATAACATTGCTGTGCT -TGATTCCCACCGTAATGGCGTTTTCCCTCAGCACAAGAGATGGCGAACCCCTCATGATAG -TGGCAAAACATGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAAT -GCACTCTCATTGCCATGGACTTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCC -CCCTACTGGTCAATACCGAACCTGAAGACATTGATTGCTGGTGCAACCTCACGTCTACCT -GGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAG -CTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGGATGTCATCGG -AAGGGGCTTGGAAGCATGCTCAGAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCG -CGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCT -TCTTTGTCCTAATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAA -ACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATG -GAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGA -CAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACA -TAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACC -AACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGT -TTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCA -ATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACA -CCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGT -CACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCA -GGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCG -TGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAG -AGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGAC -AGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCA -CAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTTAAGTGCAAAGTCC -GTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAA -TTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAG -GTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGG -TTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAG -AATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAA -CACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAG -GTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGAC -TGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGT -TTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCA -CGAACTCGAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGT -TTCTGGGCTTCACAGTTCAAGCAGACATGGGTTGTGTGGCGTCATGGAGTGGGAAAGAAT -TGAAGTGTGGAAGCGGAATTTTTGTGGTTGACAACGTGCACACTTGGACAGAACAGTACA -AATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCTGCAATATTAAATGCCCACAAAGATG -GGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAGCAAATAACCA -ACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTAGTGGCTGGGGATG -TGAAGGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCCCCAGTGAGTGATCTGAAAT -ATTCATGGAAGACATGGGGAAAAGCAAAAATCTTCACCCCAGAAGCAAGAAATAGCACAT -TTTTAATAGACGGACCAGACACCTCTGAATGCCCCAATGAACGAAGAGCATGGAACTCTC -TTGAGGTGGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTCCGAG -AAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCTGCAATTAAAGATCAGAAAG -CTGTGCATGCTGACATGGGTTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAG -AGAAAGCATCTCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACCCACACACTGTGGA -GCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAATCATATGCGGGCCCTTTTTCAC -AGCACAATTACCGCCAGGGCTATGCCACGCAAACCGTGGGCCCATGGCACTTAGGCAAAT -TAGAGATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACC -ATAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAACTAGTCACGCAATGGTGCT -GCCGCTCCTGCACGATGCCTCCCTTAAGGTTCTTGGGAGAAGATGGGTGCTGGTATGGGA -TGGAGATTAGGCCCTTGAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGACGGCCG -GACAGGGCACATCAGAAACTTTTTCTATGGGTCTGTTGTGCCTGACCTTGTTTGTGGAAG -AATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTAGTTGTGGTGATCACTCTTT -GTGCTATCATCCTGGGAGGCCTCACATGGATGGACTTACTACGAGCCCTCATCATGTTGG -GGGACACTATGTCTGGTAGAATAGGAGGACAGATCCACCTAGCCATCATGGCAGTGTTCA -AGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAG -CACTAATGGTAATAGGAATGGCCATGACAACGGTGCTTTCAATTCCACATGACCTTATGG -AACTCATTGATGGAATATCACTGGGACTAATTTTGCTAAAAATAGTAACACAGTTTGACA -ACACCCAAGTGGGAACCTTAGCTCTTTCCTTGACTTTCATAAGATCAACAATGCCATTGG -TCATGGCTTGGAGGACCATTATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTGTGCA -GGACAAGCTGTCTTCAAAAACAGTCTCATTGGGTAGAAATAACAGCACTCATCCTAGGAG -CCCAAGCTCTGCCAGTGTACCTAATGACTCTTATGAAAGGAGCCTCAAGAAGATCTTGGC -CTCTTAACGAGGGCATAATGGCTGTGGGTTTGGTTAGTCTCTTAGGAAGCGCTCTTTTAA -AGAATGATGTCCCTTTAGCTGGCCCAATGGTGGCAGGAGGCTTACTTCTGGCGGCTTACG -TGATGAGTGGTAGCTCAGCAGATCTGTCACTAGAGAAGGCCGCCAACGTGCAGTGGGATG -AAATGGCAGACATAACAGGCTCAAGCCCAATCGTAGAAGTGAAGCAGGATGAAGATGGCT -CTTTCTCCATACGGGACGTCGAGGAAACCAATATGATAACCCTTTTGGTGAAACTGGCAC -TGATAACAGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACCTTATGGTACA -TGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTCCCCTCACCCGCTGCCA -CTAAAAAAGCCGCACTGTCTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTATTCGGGA -AAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAA -CAAGAGGATCAGTGATCTGCCACGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCA -GGAATGACATGATATCATACGGTGGGGGATGGAGGCTTGGAGACAAATGGGACAAAGAAG -AAGACGTTCAGGTCCTCGCCATAGAACCAGGAAAAAATCCTAAACATGTCCAAACGAAAC -CTGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTAGATTTCAAACCCG -GAACGTCTGGTTCTCCCATCATCAACAGGAAAGGAAAAGTCATCGGACTCTATGGAAATG -GAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGAG -AGCCAGATTATGAAGTGGATGAGGACATTTTTCGAAAGAAAAGATTAACTATAATGGACT -TACACCCCGGAGCTGGAAAGACAAAAAGAATTCTTCCATCAATAGTGAGAGAAGCCTTAA -AAAGGAGGCTACGAACTTTGATTTTAGCTCCCACGAGAGTGGTGGCGGCCGAGATGGAAG -AGGCCCTACGTGGACTGCCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAG -GAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTTTTGTCATCAA -CCAGGGTTCCAAATTACAACCTTATAGTGATGGATGAAGCACATTTCACCGATCCTTCTA -GTGTCGCGGCTAGAGGATACATCTCGACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCT -TCATGACCGCAACCCCTCCCGGAGCGACAGATCCCTTTCCCCAGAGCAACAGCCCAATAG -AAGACATCGAGAGGGAAATTCCGGAAAGGTCATGGAACACAGGGTTCGACTGGATAACAG -ACTACCAAGGGAAAACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAA -ATTGTTTGAGAAAGTCGGGAAAGAAAGTTATCCAGTTGAGTAGGAAAACCTTTGATACAG -AGTATCCAAAAACGAAACTCACGGACTGGGACTTTGTGGTCACTACAGACATATCTGAAA -TGGGGGCCAATTTTAGAGCCGGGAGAGTGATAGACCCTAGAAGATGCCTCAAGCCAGTTA -TCCTACCAGATGGGCCAGAGAGAGTCATTTTAGCAGGTCCTATTCCAGTGACTCCAGCAA -GCGCTGCTCAGAGAAGAGGGCGAATAGGAAGGAACCCAGCACAAGAAGACGACCAATACG -TTTTCTCCGGAGACCCACTAAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGA -TGCTGCTTGACAATATCTACACCCCAGAAGGGATCATTCCAACATTGTTTGGTCCGGAAA -GGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTT -TTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCTG -CTGGCATTTCTTACGAAGATCGGGAATGGTGCTTCACAGGGGAAAGAAATAACCAAATTT -TAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAGCTAAGGC -CAAGATGGTTAGATGCACGTGTATACGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGT -TTGCCAGTGGAAGGAAGAGTATAACTCTCGACATCCTAACAGAGATTGCCAGTTTGCCAA -CTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGATAACATAGTCATGCTCCACACAACAG -AAAGAGGAGGGAGGGCCTATCAACACGCCCTGAACGAACTTCCGGAGTCACTGGAAACAC -TCATGCTTGTAGCTTTACTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTCATGCAAG -GGAAAGGAATAGGGAAATTGTCAATGGGTTTGATAACCATTGCGGTGGCTAGTGGCTTGC -TCTGGGTAGCAGAAATTCAACCCCAGTGGATAGCGGCCTCAATCATACTAGAGTTTTTTC -TCATGGTACTGTTGATACCGGAACCAGAAAAACAAAGGACCCCACAAGACAATCAATTGA -TCTACGTCATATTGACCATTCTCACCATCATTGGTCTAATAGCAGCCAACGAGATGGGGC -TGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCC -TCGATGTGGACTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACAATTC -TGACTCCCATGCTGAGACACACCATAGAAAACACGTCGGCCAACCTATCTCTAGCAGCCA -TTGCCAACCAGGCAGCCGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGG -ACCTCGGTGTGCCGCTGTTAGCAATGGGATGCTATTCTCAAGTGAACCCAACAACCTTGA -CAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGCCCAGGATTGCAGGCAA -AAGCCACAAGAGAGGCCCAGAAAAGGACAGCTGCTGGGATCATGAAAAATCCCACAGTGG -ACGGGATAACAGTAATAGATCTAGAACCAATATCCTATGACCCAAAATTTGAAAAGCAAT -TAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACAT -GGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAATCTTGACCTTGTGGGAGGGCA -ACCCGGGAAGGTTTTGGAACACGACCATAGCCGTATCCACCGCCAACATTTTCAGGGGAA -GTTACTTGGCGGGAGCTGGACTGGCTTTTTCACTCATAAAGAATGCACAAACCCCTAGGA -GGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCAT -TAGACAGAAAAGAGTTTGAAGAGTATAAAAGAAGTGGAATACTAGAAGTGGACAGGACTG -AAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTATCAAGAGGGTCCA -GTAAGATCAGATGGATTGTTGAGAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTAGATC -TTGGCTGTGGGAGAGGAGGATGGTCTTATTACATGGCGACACTCAAGAACGTGACTGAAG -TGAAAGGGTATACAAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACTTATG -GTTGGAATTTGGTCAAACTCCATTCAGGGGTTGACGTGTTCTACAAACCCACAGAGCAAG -TGGACACCCTGCTCTGTGATATTGGGGAGTCATCTTCTAATCCAACAATAGAGGAAGGAA -GAACATTAAGAGTTTTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCA -TCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAGCTGGAGAAACTGCAGAGAA -AACATGGTGGGAACCTTGTCAGATGCCCGCTGTCCAGGAACTCCACCCATGAGATGTATT -GGGTGTCAGGAGCGTCGGGAAACATTGTGAGCTCTGTGAACACAACATCAAAGATGTTGT -TGAACAGGTTCACAACAAGGCATAGGAAACCCACTTATGAGAAGGACGTAGATCTTGGGG -CAGGAACGAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAA -GGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACCTGGCATTATGATCAGGAAAACCCAT -ACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCTGCATCCTCCA -TGGTGAACGGGGTGGTAAAACTGCTAACAAAACCCTGGGATGTGATTCCAATGGTGACTC -AGTTAGCCATGACAGATACAACCCCTTTTGGGCAACAAAGAGTGTTCAAAGAGAAGGTGG -ATACCAGAACACCACAACCAAAACCCGGTACACGAATGGTTATGACCACGACAGCCAATT -GGCTGTGGGCCCTCCTTGGAAAGAAGAAAAATCCCAGACTGTGCACAAGGGAAGAGTTCA -TCTCAAAAGTTAGATCAAACGCAGCCATAGGCGCAGTCTTTCAGGAAGAACAGGGATGGA -CATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGG -CCCTACACCAGGAAGGGAAATGTGAATCGTGTGTCTATAACATGATGGGAAAACGTGAGA -AAAAGTTAGGAGAGTTTGGCAGAGCCAAGGGAAGCCGAGCAATCTGGTACATGTGGCTGG -GAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTTTTGAATGAAGATCACTGGTTTGGCA -GAGAAAATTCATGGAGTGGAGTGGAAGGGGAAGGTCTGCACAGATTGGGATATATCCTGG -AGGAGATAGACAAGAAGGATGGAGACCTAATGTATGCTGATGACACAGCAGGCTGGGACA -CAAGAATCACTGAGGATGACCTTCAAAATGAGGAACTGATCACGGAACAGATGGCTCCCC -ACCACAAGATCCTAGCCAAAGCCATTTTCAAACTAACCTATCAAAACAAAGTGGTGAAAG -TCCTCAGACCCACACCGCGGGGAGCGGTGATGGATATCATATCCAGGAAAGACCAAAGAG -GTAGTGGACAAGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTTCAACTCA -TCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGT -TGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTAAAGAGGATGG -CAATCAGTGGAGACGATTGCGTGGTGAAGCCCCTAGATGAGAGGTTTGGCACTTCCCTCC -TCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCTAAGG -GATGGAAAAACTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTTATGA -AGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCA -GAATCTCGCAGGGAGCTGGATGGAGCTTAAGAGAAACAGCCTGCCTGGGCAAAGCTTACG -CCCAGATGTGGTCGCTTATGTACTTCCACAGAAGGGATCTGCGTTTAGCCTCCATGGCCA -TATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACG -CTCATCACCAGTGGATGACCACTGAAGATATGCTCAAAGTGTGGAACAGAGTGTGGATAG -AAGACAACCCTAATATGACTGACAAGACTCCAGTCCATTCGTGGGAAGATATACCTTACC -TAGGGAAAAGAGAGGATTTGTGGTGTGGATCCCTGATTGGACTTTCTTCCAGAGCCACCT -GGGCGAAGAACATTCATACGGCCATAACCCAGGTCAGGAACCTGATCGGAAAAGAGGAAT -ACGTGGATTACATGCCAGTAATGAAAAGATACAGTGCTCCTTCAGAGAGTGAAGGAGTTC -TGTAATTACCAACAACAAACACCAAAGGCTATTGAAGTCAGGCCACTTGTGCCACGGTTT -GAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAATGGGAGGCGTAATAATCCCCAGGGAG -GCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCT -CCCATCACTGATAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTG -GTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGG -GAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGAT -GGATTGGTGTTGTTGATCCAACAGGTTCT +>Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome +AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCAAATCGGAAGCTTGCTTAACACAGTTCTAACAGTTTGTTTAAATAGAGAGCAGATCTCTGGAAAAATGAACCAACGAAAAAAGGTGGTTAGACCGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTATCAACCCCTCAAGGGTTGGTGAAGAGATTCTCAACCGGACTGTTTTCCGGGAAAGGACCCTTACGGATGGTGCTAGCATTCATCACGTTTTTGCGAGTCCTTTCCATCCCACCAACAGCAGGGATTCTGAAAAGATGGGGACAGTTGAAGAAAAACAAGGCCATCAAGATACTGACTGGATTCAGGAAGGAGATAGGCCGCATGCTGAACATCTTGAACGGGAGAAAGAGGTCAACAATAACATTGCTATGCTTGATTCCCACCGTAATGGCATTCCACTTGTCAACAAGAGATGGCGAACCCCTTATGATAGTAGCAAAACACGAAAGGGGGAGACCTCTCTTGTTTAAGACAACAGAAGGAATCAACAAATGCACTCTTATTGCCATGGACTTGGGTGAAATGTGTGAGGACACCGTCACGTATAAATGCCCTCTACTGGTCAACACCGAACCTGAAGACATTGATTGCTGGTGCAATCTCACGTCTACCTGGGTCATGTATGGGACATGTACCCAGAGCGGAGAACGGAGACGAGAGAAGCGCTCAGTAGCTTTAACACCACATTCAGGAATGGGATTGGAAACAAGGGCTGAGACATGGATGTCATCGGAAGGGGCTTGGAAACATGCCCAGAGAGTGGAGAGCTGGATACTCAGAAACCCAGGATTCGCGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCTTCTTTGTTCTAATGATGCTGGTCGCTCCATCCTACGGAATGCGATGCGTAGGAGTGGGGAACAGAGATTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACACGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAATTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACTTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCCTGTTTGGAAAAGGAGGAGTTGTGACATGTGCAAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTGGTCCAAATTGAAAACCTTGAATACACAGTGGTTGTGACAGTCCACAATGGAGACACCCACGCAGTAGGAAATGACACATCCAACCATGGAGTGACAGCCACGATAACTCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCCGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTGCCATGGACAGCAGGAGCAGACACATCAGAAGTCCATTGGAATTATAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTAAAGTGCAAAGTACGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAGGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTACTGGAGCTCCATGCAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGCATCATTTCATCTACTCCTTTTGCTGAGAATACCAACAGTGTAACCAATATTGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTTAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGTGGACTGTTCACATCATTGGGAAAAGCTGTGCACCAGGTTTTTGGTAGTGTCTACACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATCGGCACGAACTCAAGAAACACTTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGTTTCACGGTTCAAGCAGACATGGGTTGTGTGGTGTCATGGAGTGGGAAAGAATTGAAATGTGGAAGTGGAATTTTTGTGATTGACAACGTGCACACTTGGACAGAACAGTACAAATTTCAACCAGAGTCCCCAGCGAGACTAGCGTCCGCAATATTGAATGCCCACAAAGATGGGGTCTGTGGAATTAGATCAACCACGAGGCTGGAAAATGTCATGTGGAAACAAATAACCAACGAGCTAAACTATGTTCTCTGGGAAGGAGGACATGACCTCACTGTGGTGGCCGGGGATGTGAAAGGGGTGTTGACCAAAGGCAAGAGAGCACTCACACCTCCAGTGAATGATTTGAAATATTCATGGAAGACATGGGGGAAAGCAAAAATCTTTACTCCAGAAGCAAGAAATAGCACATTCTTGATAGACGGACCAGACACCTCCGAATGCCCCAATGAACGAAGAGCATGGAACTTTCTTGAGGTAGAAGACTATGGATTTGGCATGTTCACGACCAACATATGGATGAAATTTCGAGAAGGAAGTTCAGAAGTGTGTGACCACAGGTTAATGTCAGCGGCAATCAAAGATCAGAAAGCCGTGCATGCTGACATGGGCTATTGGATAGAGAGCTCAAAAAACCAGACCTGGCAGATAGAGAAAGCATCCCTTATTGAAGTGAAAACATGTCTGTGGCCCAAGACTCACACATTGTGGAGCAATGGAGTGCTGGAAAGCCAGATGCTCATTCCAAAAGCATATGCAGGCCCCTTTTCACAGCACAATTACCGCCAGGGCTATGCCACGCAGACCATGGGCCCATGGCACTTGGGCAAATTGGAAATAGACTTTGGAGAATGCCCCGGAACAACAGTCACAATTCAGGAGGATTGTGACCACAGAGGCCCATCTTTGAGGACCACCACTGCATCTGGAAAATTGGTCACACAGTGGTGCTGCCGCTCCTGCACGATGCCTCCCTTAAGGTTTTTGGGAGAGGATGGGTGTTGGTATGGGATGGAAATTAGGCCCTTAAGTGAAAAAGAAGAGAACATGGTCAAATCACAGGTGTCGGCCGGACAGGGTTCATCAGAAACTTTTTCTATGGGGCTGTTATGTCTGACCCTGTTCATGGAAGAATGCTTGAGGAGAAGAGTCACTAGGAAACACATGATATTGGTTGTGGTGACCACCCTTTGTGCCATCATCCTAGGAGGTCTCACGTGGATGGACTTACTACGAGCCATTATCATGTTAGGGGACACCATGTTTGGTAGAATGGGAGGACAGATTCACCTAGCCATCATGGCAGTGTTCAAGATGTCACCAGGATACGTGCTGGGTGTGTTTTTAAGGAAACTCACTTCAAGAGAGACAGCACTAATGGTGATAGGAATGGCCATGACAACGGTGTTTTCAATTCCACATGACCTTATGGAATTCATTGATGGAATATCATTGGGGCTAATCTTGCTGAAAATGGTAACACATTTTGACAACACCCAAGTGGGAACTTTAGCCCTTTCCTTAACTTTCATAAGATCAACAATGCCATTGATCATGGCTTGGAGGACCATCATGGCTGTGTTGTTTGTGGTCACACTCATTCCTTTATGTAGGACAAGCTGTCTTCAAAAGCAGTCCCACTGGGTAGAAATAACAGCAATCATCTTAGGAGCCCAGGCTCTGCCAGTGTACTTAATGACTCTCATGAAAGGAGCCTCAAAAAGATCTTGGCCTCTTAACGAGGGCATAATGGCTGTGGGCTTGGTCAGTCTCTTGGGAAGCGCCCTTCTAAAGAATGATGTCCCTTTGGCTGGTCCAATGGTGGCAGGAGGTTTACTTCTGGCAGCCTACGTGATGAGTGGTAGCTCAGCAGACCTGTCACTAGAGAAGGCCGCCAATGTGCAGTGGGATGAGATGGCAGACATAACAGGCTCAAGCCCAATCATAGAAGTGAAGCAGGATGAAGATGGCTCTTTCTCCATACGGGACGTCGAGGAAACCAACATGATAACCCTTTTGGTGAAACTGGCACTGATAACTGTGTCAGGTCTCTACCCCTTGGCAATTCCAGTCACAATGACTTTATGGTACATGTGGCAAGTGAAAACACAAAGATCAGGAGCCCTGTGGGACGTTCCCTCACCCGCTACCGCTCAGAAAGCCACACTGACTGAAGGAGTGTACAGGATCATGCAAAGAGGGTTGTTTGGGAAAACTCAGGTTGGAGTAGGGATACACATGGAAGGTGTATTTCACACAATGTGGCATGTAACAAGAGGATCAGTGATCTGCCATGAGACTGGGAGATTGGAGCCATCTTGGGCTGACGTCAGGAACGACATGATATCATACGGTGGGGGATGGAGGCTCGGAGACAAATGGGACAAAGAAGAAGATGTTCAGGTCCTAGCCATAGAACCAGGAAAAAATCCGAAACATGTCCAAACGAAACCCGGCCTTTTCAAGACCCTAACTGGAGAAATTGGAGCAGTAACATTGGATTTCAAACCCGGAACATCTGGTTCTCCCATCATTAACAAGAAAGGAAAAGTTATCGGACTCTATGGAAATGGAGTAGTTACCAAATCAGGTGATTACGTCAGTGCCATAACGCAAGCCGAAAGAATTGGTGAGCCAGATTATGAAGTGGATGAGGACATCTTTCGAAAGAAAAGATTAACCATAATGGACTTACACCCCGGAGCTGGCAAGACAAAAAGAATTCTCCCATCAATAGTCAGAGAAGCTCTAAAAAGGAGGCTGCGAACCCTGATTTTGGCTCCCACGAGAGTGGTGGCAGCCGAGATGGAAGAGGCCCTTCGCGGACTACCAATCCGTTATCAGACCCCAGCTGTGAAATCAGAACACACAGGAAGAGAGATTGTAGACCTCATGTGTCATGCAACCTTCACAACAAGACTCTTGTCATCAACCAGAGTTCCAAATTACAACCTCATAGTAATGGATGAAGCGCATTTCACAGACCCTTCTAGTGTCGCAGCTAGAGGATACATCTCAACCAGGGTGGAAATGGGAGAGGCAGCAGCCATCTTCATGACTGCAACCCCTCCCGGAGCAACAGATCCCTTCCCCCAGAGCAACAGCCCAATAGAAGACATCGAGAGAGAAATTCCAGAAAGGTCATGGAATACAGGATTCGACTGGATAACAGACTACCAAGGGAAGACTGTGTGGTTTGTTCCCAGCATAAAAGCTGGAAATGACATTGCAAATTGCTTGAGAAAGTCGGGAAAGAAGGTGATCCAGTTGAGTAGGAAAACCTTTGACACAGAGTATCCAAAAACGAAACTCACAGACTGGGATTTTGTGGTCACCACAGACATATCTGAAATGGGGGCCAATTTTAGAGCTGGGAGAGTGATAGACCCCAGGAGATGCCTCAAGCCAGTCATCCTAACAGATGGGCCAGAGAGAGTCATTTTGGCAGGTCCCATTCCAGTGACTCCAGCAAGCGCTGCTCAGAGAAGAGGGCGAATAGGTAGAAACCCAGCACAAGAAGACGACCAGTATGTCTTCTCTGGAGACCCATTGAAAAATGATGAAGATCATGCCCACTGGACAGAAGCAAAGATGCTGCTTGACAATATCTACACCCCGGAAGGGATCATTCCAACATTGTTTGGTCCGGAAAGGGAAAAAACCCAAGCCATTGATGGAGAGTTTCGCCTCAGAGGGGAACAAAGGAAGACTTTTGTGGAATTAATGAGGAGAGGAGACCTTCCGGTGTGGCTGAGCTATAAGGTAGCTTCAGCTGGTATTTCTTACAAAGACCGGGAATGGTGCTTCACAGGGGAAAGGAATAACCAAATTTTAGAAGAAAACATGGAGGTTGAAATTTGGACTAGAGAGGGAGAAAAGAAAAAACTAAGACCAAAATGGTTAGATGCACGTGTCTATGCTGACCCCATGGCTTTGAAGGATTTCAAGGAGTTTGCTAGTGGAAGAAAGAGCATAACCCTTGACATCCTGACAGAGATTGCCAGCTTGCCAACTTACCTTTCCTCTAGGGCCAAGCTCGCCCTTGACAACATAGTCATGCTCCACACAACAGAAAGGGGAGGGAGGGCCTACCAACACGCCCTGAACGAACTCCCGGAGTCATTGGAAACACTCATGCTTGTAGCTTTATTAGGTGCTATGACAGCAGGCATCTTCCTGTTTTTTATGCAAGGAAAAGGGATAGGGAAACTGTCAATGGGTTTGATAGCTATTGCGGTAGCTAGTGGCTTACTCTGGGTAGCAGAAATTCAGCCCCAGTGGATAGCGGCCTCAATCATACTGGAGTTTTTTCTCATGGTGCTGTTGATACCAGAACCAGAAAAACAAAGGACCCCACAAGACAACCAGTTGATCTATGTCATACTGGCCATTCTCACCATTATTGGTCTCATAGCAGCCAACGAGATGGGGCTGATTGAAAAAACAAAAACGGATTTTGGGTTTTACCAGGTAAAAACAGAAACCACCATCCTCGATGTGGATTTGAGACCAGCTTCAGCATGGACGCTCTATGCAGTAGCCACCACTATTCTGACTCCCATGCTGAGACACACCATAGAAAACACATCTGCCAACCTATCTCTGGCGGCCATTGCCAATCAAGCAGCTGTCCTAATGGGGCTTGGAAAAGGATGGCCGCTCCACAGAATGGACCTTGGTGTGCCGCTGTTAGCAATGGGATGTTATTCTCAAGTGAACCCAACAACTTTGACAGCATCCTTAGTCATGCTTTTAGTCCATTATGCAATAATAGGTCCAGGATTGCAGGCAAAAGCCACAAGAGAGGCTCAGAAAAGGACAGCTGCTGGGATCATGAAGAACCCCACGGTGGATGGAATAACAGTAATAGATCTAGAACCAATATCTTATGACCCAAAGTTTGAAAAGCAATTAGGGCAGGTCATGCTACTAGTCTTGTGTGCTGGACAACTACTCTTGATGAGAACAACATGGGCTTTCTGTGAAGTCTTGACTTTGGCCACAGGACCAGTCTTAACTTTGTGGGAGGGCAACCCGGGAAGATTTTGGAACACGACTATAGCCGTATCCACTGCCAACATTTTCAGGGGAAGCTACTTGGCGGGAGCTGGACTGGCTTTCTCACTCATAAAGAATGCACAAACCCCCAGGAGGGGAACTGGGACCACAGGAGAGACACTGGGAGAGAAGTGGAAGAGACAGCTAAACTCATTAGATAGGAAGGAGTTTGAAGAGTACAAGAGAAGTGGAATACTAGAAGTGGACAGGACTGAAGCCAAGTCTGCCCTGAAAGATGGGTCTAAAATCAAGCATGCAGTGTCCAGAGGGTCCAGCAAGATCAGATGGATTGTTGAAAGAGGGATGGTAAAGCCAAAAGGGAAAGTTGTGGATCTTGGTTGCGGGAGAGGAGGATGGTCGTATTACATGGCGACACTCAAGAACGTGACTGAGGTGAAAGGGTACACGAAAGGAGGTCCAGGACATGAAGAACCGATTCCCATGGCTACCTATGGCTGGAATTTGGTCAAGCTCCATTCAGGGGTTGACGTGTTCTACAAACCCACTGAGCAAGTGGACACCCTGCTCTGTGATATTGGAGAGTCATCTTCTAATCCGACAATAGAGGAAGGAAGAACATTAAGAGTTCTGAAGATGGTGGAGCCATGGCTCTCTTCAAAACCTGAATTCTGCATCAAAGTCCTTAACCCCTACATGCCAACAGTCATAGAAGAACTGGAGAAACTGCAGAGAAAGCATGGTGGAAGTCTTATCAGATGCCCGCTATCCAGGAATTCCACTCATGAGATGTATTGGGTGTCAGGTGCGTCGGGAAACATCGTGAGCTCTGTGAACACAACATCAAAGATGCTGTTGAACAGGTTTACCACGAGGCATAGGAAACCCACCTATGAGAAGGACGTAGACCTTGGAGCAGGAACAAGAAGTGTCTCCACTGAAACAGAAAAACCAGACATGACAATCATTGGGAGAAGGCTTCAGCGATTGCAAGAAGAGCACAAAGAAACTTGGCACTATGATCAGGAAAATCCATACAGAACCTGGGCGTATCATGGAAGCTATGAAGCTCCTTCGACAGGCTCAGCATCCTCCATGGTAAACGGGGTAGTAAAACTGCTGACAAAACCTTGGGACGTGATTCCAATGGTGACCCAGTTAGCCATGACAGACACAACCCCCTTTGGGCAACAAAGAGTGTTTAAAGAGAAGGTGGACACCAGAACACCACAACCAAAACCAGGCACACGAGTGGTTATGACCACAACAGCCAATTGGCTGTGGGCCCTCCTTGGGAGGAAGAAAAATCCCAGACTGTGCACGAGGGAAGAGTTCATCTCAAAAGTTAGGTCAAACGCAGCCATAGGTGCAGTCTTTCAGGAAGAACAGGGATGGACATCAGCCAGTGAAGCTGTGAATGACAGCCGGTTTTGGGAACTGGTTGACAAAGAAAGGGCTCTGCACCAGGAAGGGAAATGTGAATCGTGTGTCTACAACATGATGGGAAAACGTGAGAAAAAACTAGGAGAGTTTGGTAGAGCCAAAGGAAGCCGAGCAATCTGGTACATGTGGCTGGGAGCGCGGTTTCTGGAATTTGAAGCCCTGGGTTTCTTAAATGAAGATCACTGGTTTGGCAGAGAAAATTCATGGAGTGGAGTGGAAGGAGAAGGTCTGCATAGATTGGGATACATCCTAGAGGACATAGACAAGAAGGATGGAGACCTGATGTATGCTGATGACACAGCAGGTTGGGACACAAGAATCACTGAAGATGACCTTCTAAATGAAGAACTGATCACGGAACAGATGGCCCCTCATCATAAGATCTTAGCCAAAGCCATTTTCAAACTAACTTATCAAAACAAAGTGGTAAAAGTCCTCAGACCCACACCGAAAGGAGCGGTGATGGACATCATATCCAGGAAAGACCAAAGAGGTAGTGGACAGGTTGGAACATATGGTTTGAACACATTCACCAACATGGAAGTACAACTCATCCGCCAAATGGAAGCTGAAGGAGTCATCACACAAGATGACATGCAGAACCCAAAAGGGCTGAAAGAAAGAGTTGAGAAATGGCTGAAAGAGTGTGGTGTCGACAGGTTGAAGAGGATGGCAATCAGTGGAGATGATTGTGTGGTGAAGCCCCTGGATGAGAGGTTCAGCACTTCCCTCCTCTTCTTGAACGACATGGGAAAGGTGAGGAAAGACATTCCGCAGTGGGAACCATCCAAGGGATGGAAAAATTGGCAAGAGGTTCCTTTTTGCTCCCACCACTTTCACAAGATCTTCATGAAGGATGGCCGCTCACTAGTTGTTCCATGTAGAAACCAGGATGAACTGATAGGGAGAGCCAGAATCTCGCAGGGGGCTGGATGGAGCTTAAAAGAAACAGCCTGTCTGGGCAAAGCTTACGCCCAGATGTGGTCGCTCATGTATTTTCACAGAAGGGACCTGCGTTTAGCCTCCATGGCCATATGCTCAGCAGTTCCAACGGAATGGTTTCCAACAAGCAGAACAACATGGTCAATCCACGCCCACCATCAGTGGATGACCACTGAAGACATGCTCAAAGTGTGGAACAGAGTGTGGATAGAAGACAACCCTAACATGACTGACAAAACTCCAGTCCATTCGTGGGAAGACATACCTTACCTAGGGAAAAGAGAGGATTTGTGGTGTGGATCCTTGATTGGACTTTCTTCCAGAGCCACCTGGGCGAAAAACATTCACACAGCCATAACCCAAGTCAGGAACCTGATCGGGAAAGAGGAGTATGTGGATTACATGCCAGTCATGAAAAGATACAGCGCTCCTTTCGAGAGTGAAGGAGTTCTGTAATTACCAACAACAAACACCAAAGCCTATTGAAGTCAGGCCACTTGTGCCACGGCTTGAGCAAACCGTGCTGCCTGTAGCTCCGCCAATAACGGGAGGCGTAAAAATTCCCAGGGAGGCCATGCGCCACGGAAGCTGTACGCGTGGCATATTGGACTAGCGGTTAGAGGAGACCCCTCCCATCACTGACAAAACGCAGCAAAAGGGGGCCCGAAGCCAGGAGGAAGCTGTACTCCTGGTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCAACACAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCTGCAACATCAATCCAGGCACAGAGCGCCGCAAGATGGATTGGTGTTGTTGATCCAACAGGTTCT diff --git a/nextclade/rules/annotate_phylogeny.smk b/nextclade/rules/annotate_phylogeny.smk index ff8afcc9..a162561f 100644 --- a/nextclade/rules/annotate_phylogeny.smk +++ b/nextclade/rules/annotate_phylogeny.smk @@ -26,7 +26,7 @@ rule ancestral: input: tree = "results/{gene}/tree_{serotype}.nwk", alignment = "results/{gene}/aligned_{serotype}.fasta", - root_sequence = lambda wildcard: "../phylogenetic/config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb", + root_sequence = "resources/{serotype}/reference.fasta", output: node_data = "results/{gene}/nt-muts_{serotype}.json" params: @@ -47,7 +47,7 @@ rule translate: input: tree = "results/{gene}/tree_{serotype}.nwk", node_data = "results/{gene}/nt-muts_{serotype}.json", - reference = lambda wildcard: "../phylogenetic/config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb" + reference = "resources/{serotype}/genome_annotation.gff3", output: node_data = "results/{gene}/aa-muts_{serotype}.json" shell: diff --git a/nextclade/rules/construct_phylogeny.smk b/nextclade/rules/construct_phylogeny.smk index 636cfd46..8cd3f138 100644 --- a/nextclade/rules/construct_phylogeny.smk +++ b/nextclade/rules/construct_phylogeny.smk @@ -46,6 +46,11 @@ rule refine: date_inference = "marginal", clock_filter_iqd = 4, strain_id = config.get("strain_id_field", "strain"), + root_flag = lambda wildcard: ( + f"--root '{config['refine']['root_id'][wildcard.serotype]}'" + if wildcard.serotype in config["refine"]['root_id'] + else "" + ) shell: """ augur refine \ @@ -55,9 +60,8 @@ rule refine: --metadata-id-columns {params.strain_id} \ --output-tree {output.tree} \ --output-node-data {output.node_data} \ - --timetree \ - --coalescent {params.coalescent} \ - --date-confidence \ - --date-inference {params.date_inference} \ - --clock-filter-iqd {params.clock_filter_iqd} + --divergence-unit mutations \ + --keep-polytomies \ + --use-fft \ + {params.root_flag} """ \ No newline at end of file diff --git a/nextclade/rules/prepare_sequences.smk b/nextclade/rules/prepare_sequences.smk index 38a13b90..4a00795a 100644 --- a/nextclade/rules/prepare_sequences.smk +++ b/nextclade/rules/prepare_sequences.smk @@ -85,7 +85,7 @@ rule align: """ input: sequences = "results/{gene}/filtered_{serotype}.fasta", - reference = lambda wildcard: "../phylogenetic/config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb" + reference = "resources/{serotype}/reference.fasta", output: alignment = "results/{gene}/aligned_{serotype}.fasta" shell: @@ -95,6 +95,5 @@ rule align: --reference-sequence {input.reference} \ --output {output.alignment} \ --fill-gaps \ - --remove-reference \ --nthreads 1 """