Mercurial > repos > iuc > hyphy_annotate
view test-data/summary/ORF6.SLAC.json @ 6:68cd2d8e3840 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"
author | iuc |
---|---|
date | Sat, 03 Jul 2021 08:52:12 +0000 |
parents | 1669328e2ab1 |
children |
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"Inferred non-synonymous susbsitution rate"], ["dN-dS", "Scaled by the length of the tested branches"], ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with P<sub>s</sub> probability of success"], ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with P<sub>s</sub> probability of success"], ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] ] }, "analysis":{ "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", "contact":"spond@temple.edu", "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", "requirements":"in-frame codon alignment and a phylogenetic tree", "version":"2.00" }, "branch attributes":{ "0":{ "Node100":{ "Global MG94xREV":0.005590443923023665, "Nucleotide GTR":0.005480709230504446, "amino-acid": [ ["M", "F", "H", "R", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CGC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node112":{ "Global MG94xREV":0.005589329527185063, "Nucleotide GTR":0.005479616709115599, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], 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count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node119":{ "Global MG94xREV":0.005587606452217953, "Nucleotide GTR":0.00547792745634657, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "L", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "CTT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node206":{ "Global MG94xREV":0.005612056496775136, "Nucleotide GTR":0.005501897571553138, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTT", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node252":{ "Global MG94xREV":0.005583030691028247, "Nucleotide GTR":0.005473441512665834, "amino-acid": [ ["M", "L", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "CTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node264":{ "Global MG94xREV":0.005587464466527973, "Nucleotide GTR":0.005477788257690359, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "T", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ACA", "AAC", "CTC", "ATA", "ATT", 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0, 0, 0, 0, 0] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node292":{ "Global MG94xREV":0.005554543997601957, "Nucleotide GTR":0.00544551398387603, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "S", "Q", "V", "T", "I", "A", "E", "M", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TCT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATG", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node33":{ "Global MG94xREV":0.01150596024374743, "Nucleotide GTR":0.01128011002024621, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "L"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node342":{ "Global MG94xREV":0.005674088416594295, "Nucleotide GTR":0.005562711868274484, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "V", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "GTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node36":{ "Global MG94xREV":0.00555719971553566, "Nucleotide GTR":0.005448117572784753, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTC", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", 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0] ] }, "Node62":{ "Global MG94xREV":0.005614641057622094, "Nucleotide GTR":0.005504431400115917, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "Y"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "TAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "Node71":{ "Global MG94xREV":0.00558913002817074, "Nucleotide GTR":0.00547942112606274, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "N", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAC", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "REFERENCE":{ "Global MG94xREV":0, "Nucleotide GTR":0, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"REFERENCE", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1284652_hCoV_19_Germany_SN_RKI_I_038291_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "T", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ACA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1284652/hCoV-19/Germany/SN-RKI-I-038291/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1442952_hCoV_19_Singapore_321_2021":{ "Global MG94xREV":0.00557872293700733, "Nucleotide GTR":0.00546921831544746, "amino-acid": [ ["M", "F", "H", "L", "V", "G", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GGC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1442952/hCoV-19/Singapore/321/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1470937_hCoV_19_USA_NY_PRL_2021_03_29_01C17_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAC"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1470937/hCoV-19/USA/NY-PRL-2021_03_29_01C17/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1512225_hCoV_19_USA_GA_CDC_STM_000041012_2021":{ "Global MG94xREV":0.005614165833101072, "Nucleotide GTR":0.005503965503765864, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "S", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGT", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1512225/hCoV-19/USA/GA-CDC-STM-000041012/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1516887_hCoV_19_Australia_QLD1826_2021":{ "Global MG94xREV":0.005608121500950802, "Nucleotide GTR":0.005498039815669468, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "H", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAT", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1516887/hCoV-19/Australia/QLD1826/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ "Global MG94xREV":0.0112203283279825, "Nucleotide GTR":0.0110000847666501, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "C"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATC", "TGT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] ], "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0] ] }, "epi_isl_1533799_hCoV_19_India_MH_NCCS_9947_2021":{ "Global MG94xREV":0.005586229046527186, "Nucleotide GTR":0.005476577087719768, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAC", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1533799/hCoV-19/India/MH-NCCS-9947/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ "Global MG94xREV":0, "Nucleotide GTR":0, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "F", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TTT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1589923_hCoV_19_India_WB_1930300571091_2021":{ "Global MG94xREV":0.005614064105565932, "Nucleotide GTR":0.005503865773038113, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "K", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AAG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1589923/hCoV-19/India/WB-1930300571091/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1589926_hCoV_19_India_WB_1930300586246_2021":{ "Global MG94xREV":0.005612040471290908, "Nucleotide GTR":0.005501881860632767, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "F", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "TTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"epi_isl_1589926/hCoV-19/India/WB-1930300586246/2021", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "epi_isl_1631286_hCoV_19_England_CAMC_14E7527_2021":{ "Global MG94xREV":0.005611861400289367, "Nucleotide GTR":0.005501706304611714, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "L", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", 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"Nucleotide GTR":0.005503988159180567, "amino-acid": [ ["M", "F", "H", "L", "F", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "TTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "gb_MT326182_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_1365_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.005652259542238793, "Nucleotide GTR":0.005541311472381236, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTT", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"gb_MT326182_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_1365_2020_Segment_null_Host_Human", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "gb_MT358638_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_DEU_FFM1_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.005583605362239691, "Nucleotide GTR":0.005474004903669556, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "A", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GCT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT"] ], "nonsynonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ], "original name":"gb_MT358638_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_DEU_FFM1_2020_Segment_null_Host_Human", "synonymous substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "gb_MT359866_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_ESP_VH198152683_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.005578727966494077, "Nucleotide GTR":0.005469223246210523, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", 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substitution count": [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] }, "gb_MT969697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2890_2020_Segment_null_Host_Human":{ "Global MG94xREV":0.005656347276862861, "Nucleotide GTR":0.005545318968958342, "amino-acid": [ ["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "V", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D"] ], "codon": [ ["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GTG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", 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