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]
}
}
},
"headers": [
["ES", "Expected synonymous sites"],
["EN", "Expected non-synonymous sites"],
["S", "Inferred synonymous substitutions"],
["N", "Inferred non-synonymous substitutions"],
["P[S]", "Expected proportion of synonymous sites"],
["dS", "Inferred synonymous susbsitution rate"],
["dN", "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 Ps probability of success"],
["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps 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":{
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"Nucleotide GTR":0.008829588063259819,
"amino-acid": [
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],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "---", "ACG", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGT", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
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],
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},
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"Nucleotide GTR":0.3164363257320967,
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],
"codon": [
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],
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],
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]
},
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"Nucleotide GTR":0.00411336547932549,
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],
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],
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],
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]
},
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"Nucleotide GTR":0.02685530439572239,
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],
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],
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],
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]
},
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"Nucleotide GTR":0.6323101625828952,
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["S", "G", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
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],
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],
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},
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"Nucleotide GTR":0.9705535002603676,
"amino-acid": [
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],
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],
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],
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],
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"Nucleotide GTR":0.008607729673233254,
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"Nucleotide GTR":0.002892849643893717,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
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"original name":"epi_isl_415435_Wales_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416567_unknown_20200215_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["R", "W", "A", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"original name":"epi_isl_416567_unknown_20200215_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.02389441408555863,
"Nucleotide GTR":0.02164507467156026,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "A", "F", "P", "F", "-", "M", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"original name":"epi_isl_416604_unknown_20200216_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416677_Washington_20200312_null_1":{
"Global MG94xREV":0.009744892933010478,
"Nucleotide GTR":0.008827541635718677,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "V", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"original name":"epi_isl_416677_Washington_20200312_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417222_England_20200304_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "KN", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"original name":"epi_isl_417222_England_20200304_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418182_Madrid_20200312_null_3":{
"Global MG94xREV":0.03624415473654596,
"Nucleotide GTR":0.03283225246164395,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 2.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_418182_Madrid_20200312_null_3",
"synonymous substitution count": [
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]
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"epi_isl_418999_Singapore_20200301_null_4":{
"Global MG94xREV":179.7867900465606,
"Nucleotide GTR":162.8622690468015,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_418999_Singapore_20200301_null_4",
"synonymous substitution count": [
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]
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"epi_isl_419835_Northern_Territory_20200224_null_18":{
"Global MG94xREV":0.009744908946686491,
"Nucleotide GTR":0.008827556141921341,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_419835_Northern_Territory_20200224_null_18",
"synonymous substitution count": [
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]
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"epi_isl_421881_England_20200326_null_5":{
"Global MG94xREV":0.009743095037962585,
"Nucleotide GTR":0.008825912988436355,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_421881_England_20200326_null_5",
"synonymous substitution count": [
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]
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"epi_isl_421889_England_20200327_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421889_England_20200327_null_1",
"synonymous substitution count": [
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]
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"epi_isl_422051_Wales_20200330_null_1":{
"Global MG94xREV":0.009747243285061288,
"Nucleotide GTR":0.008829670733568168,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422051_Wales_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422206_Wales_20200330_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422206_Wales_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422359_Wales_20200324_null_1":{
"Global MG94xREV":0.009750999386441259,
"Nucleotide GTR":0.008833073248254322,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "I", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_422359_Wales_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422425_Zhejiang_20200124_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "EDAGV", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_422425_Zhejiang_20200124_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422636_Prague_20200308_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "C", "K", "I", "N", "F", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_422636_Prague_20200308_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422725_Netherlands_20200323_null_8":{
"Global MG94xREV":0.009687148463882746,
"Nucleotide GTR":0.008775233035823171,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422725_Netherlands_20200323_null_8",
"synonymous substitution count": [
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]
},
"epi_isl_422985_Washington_20200317_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "C", "K", "IM", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_422985_Washington_20200317_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423309_England_20200325_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "KQE", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
"original name":"epi_isl_423309_England_20200325_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423534_England_20200331_null_4":{
"Global MG94xREV":0.002087749346869896,
"Nucleotide GTR":0.001891215676881227,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "L", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
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"original name":"epi_isl_423534_England_20200331_null_4",
"synonymous substitution count": [
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]
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"epi_isl_423536_England_20200331_null_1":{
"Global MG94xREV":0.009695448885291056,
"Nucleotide GTR":0.008782752083603323,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_423536_England_20200331_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423770_England_20200322_null_1":{
"Global MG94xREV":0.009701802800803468,
"Nucleotide GTR":0.00878850786297629,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "T", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"original name":"epi_isl_423770_England_20200322_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423807_England_20200324_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "Y"]
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"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_423807_England_20200324_null_2",
"synonymous substitution count": [
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]
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"epi_isl_423904_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "ILV", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423904_England_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_424158_England_20200321_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424158_England_20200321_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424288_Washington_20200322_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "V", "K", "L", "I", "L", "V", "V", "L", "S", "P", "C", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_424288_Washington_20200322_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424315_Idaho_20200320_null_1":{
"Global MG94xREV":0.3540574064182323,
"Nucleotide GTR":0.3207276383719048,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "EDAGV", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424315_Idaho_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424366_Kayseri_20200317_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424366_Kayseri_20200317_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_424479_Reykjavik_20200320_null_1":{
"Global MG94xREV":1.048029231063658,
"Nucleotide GTR":0.9493713000504574,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "Y", "G", "R", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424479_Reykjavik_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424600_Reykjavik_20200327_null_1":{
"Global MG94xREV":0.009693251000706034,
"Nucleotide GTR":0.008780761100447513,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "R", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424600_Reykjavik_20200327_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_425131_Duesseldorf_20200320_null_1":{
"Global MG94xREV":0.009753575042576306,
"Nucleotide GTR":0.008835406440822768,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "Y", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425131_Duesseldorf_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_425251_England_20200331_null_1":{
"Global MG94xREV":0.009702297909516181,
"Nucleotide GTR":0.008788956363827526,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_425251_England_20200331_null_1",
"synonymous substitution count": [
[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]
]
},
"epi_isl_426014_Scotland_20200401_null_13":{
"Global MG94xREV":0.009744102432612868,
"Nucleotide GTR":0.008826825550357766,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "S", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"original name":"epi_isl_426014_Scotland_20200401_null_13",
"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]
]
},
"epi_isl_426103_Washington_20200323_null_2":{
"Global MG94xREV":0.4372954585439896,
"Nucleotide GTR":0.3961299414928738,
"amino-acid": [
["L", "G", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"original name":"epi_isl_426103_Washington_20200323_null_2",
"synonymous substitution count": [
[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]
]
},
"epi_isl_426899_Northern_territory_20200327_null_2":{
"Global MG94xREV":0.009746169309020383,
"Nucleotide GTR":0.008828697858003288,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "I", "-"]
],
"codon": [
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],
"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, 1, 0]
],
"original name":"epi_isl_426899_Northern_territory_20200327_null_2",
"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]
]
},
"epi_isl_426949_Victoria_20200328_null_1":{
"Global MG94xREV":0.009758602428671282,
"Nucleotide GTR":0.00883996056577593,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "I", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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, 1, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426949_Victoria_20200328_null_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]
]
},
"epi_isl_427271_Arizona_20200323_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "D", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_427271_Arizona_20200323_null_3",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 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_428341_Wisconsin_20200328_null_5":{
"Global MG94xREV":0.009719730747824343,
"Nucleotide GTR":0.00880474813363475,
"amino-acid": [
["M", "G", "Y", "L", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_428341_Wisconsin_20200328_null_5",
"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]
]
},
"epi_isl_428685_Madrid_20200327_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "T", "M", "L", "G", "R", "A", "A", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_428685_Madrid_20200327_null_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]
]
},
"epi_isl_429024_California_20200323_null_16":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_429024_California_20200323_null_16",
"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]
]
},
"epi_isl_429172_Bangkok_20200321_null_4":{
"Global MG94xREV":0.009744173899174641,
"Nucleotide GTR":0.008826890289298873,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "F", "T", "-"]
],
"codon": [
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],
"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, 1, 0, 0]
],
"original name":"epi_isl_429172_Bangkok_20200321_null_4",
"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]
]
},
"epi_isl_429235_Abruzzo_20200324_null_2":{
"Global MG94xREV":0.002085465580816448,
"Nucleotide GTR":0.001889146896848275,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "L", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_429235_Abruzzo_20200324_null_2",
"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]
]
},
"epi_isl_429464_Unknown_20200323_null_1":{
"Global MG94xREV":0.009703906851927445,
"Nucleotide GTR":0.008790413845836061,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "A", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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, 1, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_429464_Unknown_20200323_null_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]
]
},
"epi_isl_429491_Unknown_20200323_null_5":{
"Global MG94xREV":0.009744084722243817,
"Nucleotide GTR":0.00882680950718303,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "V", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_429491_Unknown_20200323_null_5",
"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]
]
},
"epi_isl_429689_Minas_gerais_20200317_null_1":{
"Global MG94xREV":0.9789172976013601,
"Nucleotide GTR":0.886765330507498,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "P", "R", "P", "R", "G", "V", "QHPRL", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "CCG", "AGG", "CCA", "CGC", "GGA", "GTA", "CNN", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2.333333333333333, 0, 0, 1, 2, 2.25, 32.83333333333333, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_429689_Minas_gerais_20200317_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.6666666666666666, 1, 0, 0, 0, 0.75, 7.166666666666666, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_430058_Utah_20200403_null_6":{
"Global MG94xREV":0.002367122891695197,
"Nucleotide GTR":0.002144289940068826,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_430058_Utah_20200403_null_6",
"synonymous substitution count": [
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]
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"epi_isl_430180_Washington_20200315_null_1":{
"Global MG94xREV":0.009704607156862038,
"Nucleotide GTR":0.008791048226430105,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "H", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
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"original name":"epi_isl_430180_Washington_20200315_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.009753067056994113,
"Nucleotide GTR":0.00883494627528702,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "F", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
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"original name":"epi_isl_430498_Victoria_20200401_null_10",
"synonymous substitution count": [
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]
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"epi_isl_430520_Victoria_20200402_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "SWL"]
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"codon": [
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],
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"original name":"epi_isl_430520_Victoria_20200402_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430566_Victoria_20200406_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430566_Victoria_20200406_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430608_Victoria_20200408_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430608_Victoria_20200408_null_1",
"synonymous substitution count": [
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"epi_isl_430709_Victoria_20200407_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_430709_Victoria_20200407_null_1",
"synonymous substitution count": [
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"epi_isl_430737_Beijing_20200225_null_5":{
"Global MG94xREV":0.009760618887313359,
"Nucleotide GTR":0.008841787201814119,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_430737_Beijing_20200225_null_5",
"synonymous substitution count": [
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]
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"epi_isl_430876_Washington_20200401_null_9":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_430876_Washington_20200401_null_9",
"synonymous substitution count": [
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]
},
"epi_isl_430896_Washington_20200329_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_430896_Washington_20200329_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430903_USA_20200405_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
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],
"original name":"epi_isl_430903_USA_20200405_null_3",
"synonymous substitution count": [
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]
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"epi_isl_430980_Washington_20200403_null_14529":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_430980_Washington_20200403_null_14529",
"synonymous substitution count": [
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]
},
"epi_isl_432226_Wales_20200404_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_432226_Wales_20200404_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_432289_Wales_20200401_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "NTSI", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
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],
"original name":"epi_isl_432289_Wales_20200401_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_432401_Wales_20200330_null_1":{
"Global MG94xREV":0.009902364516460377,
"Nucleotide GTR":0.008970189376325202,
"amino-acid": [
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],
"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_432401_Wales_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_432439_Wales_20200408_null_4":{
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"Nucleotide GTR":0.00878846185382203,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"original name":"epi_isl_432439_Wales_20200408_null_4",
"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]
]
},
"epi_isl_432653_England_20200318_null_1":{
"Global MG94xREV":0.009701816805090949,
"Nucleotide GTR":0.008788520548947467,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "S", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "---", "ACG", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TCT", "AAT", "CTC", "ACA", "---"]
],
"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, 1, 0, 0, 0, 0]
],
"original name":"epi_isl_432653_England_20200318_null_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]
]
},
"epi_isl_433319_Scotland_20200325_null_1":{
"Global MG94xREV":0.009756291526566754,
"Nucleotide GTR":0.008837867204188067,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "S", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_433319_Scotland_20200325_null_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]
]
},
"epi_isl_433486_England_20200417_null_1":{
"Global MG94xREV":0.009754551861145251,
"Nucleotide GTR":0.008836291304991827,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_433486_England_20200417_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_433657_Scotland_20200405_null_1":{
"Global MG94xREV":0.005194838833384683,
"Nucleotide GTR":0.004705814256533327,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"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]
],
"original name":"epi_isl_433657_Scotland_20200405_null_1",
"synonymous substitution count": [
[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]
]
},
"epi_isl_433714_England_20200405_null_1":{
"Global MG94xREV":0.009827217308273482,
"Nucleotide GTR":0.008902116272429881,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "Y", "F", "N", "L", "T", "-"]
],
"codon": [
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],
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],
"original name":"epi_isl_433714_England_20200405_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_434251_Washington_20200402_null_1":{
"Global MG94xREV":0.009753857296334654,
"Nucleotide GTR":0.00883566212416591,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "K", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"original name":"epi_isl_434251_Washington_20200402_null_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]
]
},
"epi_isl_434332_Washington_20200326_null_1":{
"Global MG94xREV":0.009703347508048516,
"Nucleotide GTR":0.008789907156700139,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "P", "T", "-"]
],
"codon": [
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],
"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, 1, 0, 0]
],
"original name":"epi_isl_434332_Washington_20200326_null_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]
]
},
"epi_isl_435058_KZN_20200311_null_1":{
"Global MG94xREV":0.00985988157419688,
"Nucleotide GTR":0.00893170563471646,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "Q", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution 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]
],
"original name":"epi_isl_435058_KZN_20200311_null_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]
]
}
},
"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"amino-acid":{
"attribute type":"node label",
"display order":1
},
"codon":{
"attribute type":"node label",
"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
"attribute type":"branch label",
"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":inf,
"Equilibrium frequencies": [
[0.03103620300446595],
[0.02288984779421039],
[0.01445382103622824],
[0.03632247681933937],
[0.01639969363295188],
[0.01209511650236124],
[0.007637475395606536],
[0.0191929886443083],
[0.01527018690522346],
[0.01126208170501442],
[0.007111454603067792],
[0.01787109749901259],
[0.04599295166932649],
[0.03392076225193751],
[0.02141930481188961],
[0.05382674938109278],
[0.01338837952360765],
[0.009874209466357866],
[0.006235081062315588],
[0.0156687693022494],
[0.007074490471571456],
[0.005217584447832126],
[0.003294649773488144],
[0.008279460477988101],
[0.006587244504559308],
[0.004858230372797688],
[0.003067735224475683],
[0.00770922383081935],
[0.01984041321908099],
[0.01463271904406781],
[0.009239847474645948],
[0.02321975240117114],
[0.01775079089542148],
[0.01309157894619348],
[0.008266692765768194],
[0.02077421296448893],
[0.009379611687216216],
[0.006917659478457533],
[0.004368164130671205],
[0.01097720388136048],
[0.008733603612839529],
[0.00644121503407155],
[0.004067312731624243],
[0.01022116380444525],
[0.02630512719703385],
[0.01940058059488807],
[0.01225051920128365],
[0.03078557556497966],
[0.01985502012210422],
[0.03150669740648336],
[0.01422535658629252],
[0.0104914975273151],
[0.006624868327005612],
[0.01664830536061696],
[0.009768909818893652],
[0.00616858947734268],
[0.01550167583625131],
[0.03989502198002477],
[0.02942341177295564],
[0.01857944761647213],
[0.04669018342443397]
],
"Log Likelihood":-inf,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.9165418920175951, 1]
]
},
"display order":1,
"estimated parameters":104
},
"Nucleotide GTR":{
"AIC-c":1669.140180226152,
"Equilibrium frequencies": [
[0.2998953505755718],
[0.1823889968605173],
[0.1590671251308118],
[0.3586485274330991]
],
"Log Likelihood":-682.9375812791537,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.3857301053033687,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.1755992233315752,
"Substitution rate from nucleotide C to nucleotide G":0.2821873396061184,
"Substitution rate from nucleotide C to nucleotide T":1.469462276438206,
"Substitution rate from nucleotide G to nucleotide T":0.8788244807378721
},
"display order":0,
"estimated parameters":149
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-02/sequences.ORF10.compressed.fas",
"number of sequences":72,
"number of sites":40,
"partition count":1,
"trees":{
"0":"(epi_isl_430566_Victoria_20200406_null_1,epi_isl_429172_Bangkok_20200321_null_4,(epi_isl_407073_England_20200129_null_1,epi_isl_414480_USA_20200221_null_1)Node56,(epi_isl_424158_England_20200321_null_1,epi_isl_430058_Utah_20200403_null_6)Node53,epi_isl_432226_Wales_20200404_null_1,epi_isl_423309_England_20200325_null_1,epi_isl_417222_England_20200304_null_1,epi_isl_432289_Wales_20200401_null_1,epi_isl_423770_England_20200322_null_1,epi_isl_430180_Washington_20200315_null_1,epi_isl_426949_Victoria_20200328_null_1,epi_isl_430520_Victoria_20200402_null_1,epi_isl_414934_Shandong_20200121_null_1,epi_isl_422051_Wales_20200330_null_1,(((epi_isl_418182_Madrid_20200312_null_3,epi_isl_416567_unknown_20200215_null_1,epi_isl_424479_Reykjavik_20200320_null_1)Node66,epi_isl_416604_unknown_20200216_null_1)Node65,epi_isl_424366_Kayseri_20200317_null_3)Node64,epi_isl_419835_Northern_Territory_20200224_null_18,epi_isl_435058_KZN_20200311_null_1,(epi_isl_423534_England_20200331_null_4,epi_isl_423904_England_20200318_null_1)Node79,epi_isl_432439_Wales_20200408_null_4,epi_isl_428341_Wisconsin_20200328_null_5,epi_isl_430980_Washington_20200403_null_14529,epi_isl_426014_Scotland_20200401_null_13,(epi_isl_429235_Abruzzo_20200324_null_2,epi_isl_430709_Victoria_20200407_null_1)Node87,epi_isl_432653_England_20200318_null_1,epi_isl_432401_Wales_20200330_null_1,epi_isl_430608_Victoria_20200408_null_1,epi_isl_421881_England_20200326_null_5,(epi_isl_414937_Shandong_20200126_null_1,(epi_isl_430876_Washington_20200401_null_9,(epi_isl_415435_Wales_20200306_null_1,epi_isl_428685_Madrid_20200327_null_1)Node24,(epi_isl_424288_Washington_20200322_null_1,epi_isl_430903_USA_20200405_null_3)Node27)Node22,epi_isl_418999_Singapore_20200301_null_4,(epi_isl_422425_Zhejiang_20200124_null_1,epi_isl_424315_Idaho_20200320_null_1)Node17,epi_isl_429689_Minas_gerais_20200317_null_1)Node13,epi_isl_422359_Wales_20200324_null_1,epi_isl_434332_Washington_20200326_null_1,epi_isl_423807_England_20200324_null_2,epi_isl_426899_Northern_territory_20200327_null_2,epi_isl_429464_Unknown_20200323_null_1,epi_isl_433714_England_20200405_null_1,epi_isl_429491_Unknown_20200323_null_5,epi_isl_425131_Duesseldorf_20200320_null_1,epi_isl_425251_England_20200331_null_1,epi_isl_430737_Beijing_20200225_null_5,((epi_isl_426103_Washington_20200323_null_2,epi_isl_430896_Washington_20200329_null_1)Node128,epi_isl_427271_Arizona_20200323_null_3)Node127,epi_isl_422725_Netherlands_20200323_null_8,(epi_isl_433657_Scotland_20200405_null_1,epi_isl_422206_Wales_20200330_null_1)Node113,epi_isl_433486_England_20200417_null_1,epi_isl_416677_Washington_20200312_null_1,epi_isl_424600_Reykjavik_20200327_null_1,epi_isl_433319_Scotland_20200325_null_1,epi_isl_423536_England_20200331_null_1,epi_isl_421889_England_20200327_null_1,epi_isl_430498_Victoria_20200401_null_10,((epi_isl_422636_Prague_20200308_null_1,epi_isl_422985_Washington_20200317_null_1)Node101,epi_isl_429024_California_20200323_null_16)Node100,epi_isl_434251_Washington_20200402_null_1)"
}
},
"tested":{
"0":{
"Node100":"test",
"Node101":"test",
"Node113":"test",
"Node127":"test",
"Node128":"test",
"Node13":"test",
"Node17":"test",
"Node22":"test",
"Node24":"test",
"Node27":"test",
"Node53":"test",
"Node56":"test",
"Node64":"test",
"Node65":"test",
"Node66":"test",
"Node79":"test",
"Node87":"test",
"epi_isl_407073_England_20200129_null_1":"test",
"epi_isl_414480_USA_20200221_null_1":"test",
"epi_isl_414934_Shandong_20200121_null_1":"test",
"epi_isl_414937_Shandong_20200126_null_1":"test",
"epi_isl_415435_Wales_20200306_null_1":"test",
"epi_isl_416567_unknown_20200215_null_1":"test",
"epi_isl_416604_unknown_20200216_null_1":"test",
"epi_isl_416677_Washington_20200312_null_1":"test",
"epi_isl_417222_England_20200304_null_1":"test",
"epi_isl_418182_Madrid_20200312_null_3":"test",
"epi_isl_418999_Singapore_20200301_null_4":"test",
"epi_isl_419835_Northern_Territory_20200224_null_18":"test",
"epi_isl_421881_England_20200326_null_5":"test",
"epi_isl_421889_England_20200327_null_1":"test",
"epi_isl_422051_Wales_20200330_null_1":"test",
"epi_isl_422206_Wales_20200330_null_1":"test",
"epi_isl_422359_Wales_20200324_null_1":"test",
"epi_isl_422425_Zhejiang_20200124_null_1":"test",
"epi_isl_422636_Prague_20200308_null_1":"test",
"epi_isl_422725_Netherlands_20200323_null_8":"test",
"epi_isl_422985_Washington_20200317_null_1":"test",
"epi_isl_423309_England_20200325_null_1":"test",
"epi_isl_423534_England_20200331_null_4":"test",
"epi_isl_423536_England_20200331_null_1":"test",
"epi_isl_423770_England_20200322_null_1":"test",
"epi_isl_423807_England_20200324_null_2":"test",
"epi_isl_423904_England_20200318_null_1":"test",
"epi_isl_424158_England_20200321_null_1":"test",
"epi_isl_424288_Washington_20200322_null_1":"test",
"epi_isl_424315_Idaho_20200320_null_1":"test",
"epi_isl_424366_Kayseri_20200317_null_3":"test",
"epi_isl_424479_Reykjavik_20200320_null_1":"test",
"epi_isl_424600_Reykjavik_20200327_null_1":"test",
"epi_isl_425131_Duesseldorf_20200320_null_1":"test",
"epi_isl_425251_England_20200331_null_1":"test",
"epi_isl_426014_Scotland_20200401_null_13":"test",
"epi_isl_426103_Washington_20200323_null_2":"test",
"epi_isl_426899_Northern_territory_20200327_null_2":"test",
"epi_isl_426949_Victoria_20200328_null_1":"test",
"epi_isl_427271_Arizona_20200323_null_3":"test",
"epi_isl_428341_Wisconsin_20200328_null_5":"test",
"epi_isl_428685_Madrid_20200327_null_1":"test",
"epi_isl_429024_California_20200323_null_16":"test",
"epi_isl_429172_Bangkok_20200321_null_4":"test",
"epi_isl_429235_Abruzzo_20200324_null_2":"test",
"epi_isl_429464_Unknown_20200323_null_1":"test",
"epi_isl_429491_Unknown_20200323_null_5":"test",
"epi_isl_429689_Minas_gerais_20200317_null_1":"test",
"epi_isl_430058_Utah_20200403_null_6":"test",
"epi_isl_430180_Washington_20200315_null_1":"test",
"epi_isl_430498_Victoria_20200401_null_10":"test",
"epi_isl_430520_Victoria_20200402_null_1":"test",
"epi_isl_430566_Victoria_20200406_null_1":"test",
"epi_isl_430608_Victoria_20200408_null_1":"test",
"epi_isl_430709_Victoria_20200407_null_1":"test",
"epi_isl_430737_Beijing_20200225_null_5":"test",
"epi_isl_430876_Washington_20200401_null_9":"test",
"epi_isl_430896_Washington_20200329_null_1":"test",
"epi_isl_430903_USA_20200405_null_3":"test",
"epi_isl_430980_Washington_20200403_null_14529":"test",
"epi_isl_432226_Wales_20200404_null_1":"test",
"epi_isl_432289_Wales_20200401_null_1":"test",
"epi_isl_432401_Wales_20200330_null_1":"test",
"epi_isl_432439_Wales_20200408_null_4":"test",
"epi_isl_432653_England_20200318_null_1":"test",
"epi_isl_433319_Scotland_20200325_null_1":"test",
"epi_isl_433486_England_20200417_null_1":"test",
"epi_isl_433657_Scotland_20200405_null_1":"test",
"epi_isl_433714_England_20200405_null_1":"test",
"epi_isl_434251_Washington_20200402_null_1":"test",
"epi_isl_434332_Washington_20200326_null_1":"test",
"epi_isl_435058_KZN_20200311_null_1":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":2
}
}
}