{
"MLE":{
"content":{
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"NAMES": [
["epi_isl_423372_England_20200328_null_1"],
["epi_isl_424174_Connecticut_20200313_null_1"],
["epi_isl_424964_New_York_20200401_null_1"],
["epi_isl_425293_England_20200319_null_3"],
["epi_isl_422093_Wales_20200329_null_1"],
["epi_isl_420168_South_Yorkshire_20200325_null_1"],
["epi_isl_427244_Washington_20200331_null_1"],
["epi_isl_430262_Washington_20200319_null_11769"],
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["epi_isl_423697_England_20200321_null_2"],
["epi_isl_420388_Vilvoorde_20200324_null_2"],
["epi_isl_423963_England_20200320_null_1"],
["epi_isl_430036_Utah_20200314_null_10"],
["epi_isl_430289_Washington_20200311_null_14"],
["epi_isl_429398_Unknown_20200309_null_3"],
["epi_isl_429628_USA_20200406_null_1"],
["epi_isl_419546_Duesseldorf_20200315_null_1"],
["epi_isl_429787_Luxembourg_20200322_null_17"],
["Node90"],
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["Node82"],
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["epi_isl_423802_England_20200223_null_1"],
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["epi_isl_423125_England_20200324_null_1"],
["epi_isl_421808_England_20200325_null_1"],
["epi_isl_423368_England_20200329_null_1"],
["epi_isl_425575_England_20200324_null_1"],
["epi_isl_417952_Madrid_20200309_null_1"],
["epi_isl_430097_St_Petersburg_20200414_null_1"],
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["Node75"],
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["Node74"],
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[0.5135303050145519, 2.486469694985448, 0, 0, 0.171176768338184, 0, 0, 0, 1, 1, 0.3104046019593815],
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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":{
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"Nucleotide GTR":0.005469923505725722,
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],
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],
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],
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],
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],
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]
},
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"Nucleotide GTR":0.005495243902583479,
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],
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]
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"Global MG94xREV":0.005630441247987693,
"Nucleotide GTR":0.005507772350809919,
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["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "T", "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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],
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]
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"Node90":{
"Global MG94xREV":0.004576756457852193,
"Nucleotide GTR":0.004477043905565702,
"amino-acid": [
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],
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]
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"Nucleotide GTR":0,
"amino-acid": [
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],
"original name":"epi_isl_414010_England_20200226_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005622205493237178,
"Nucleotide GTR":0.005499716026215613,
"amino-acid": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_415655_Wales_20200312_null_1",
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"epi_isl_416636_Washington_20200312_null_1":{
"Global MG94xREV":0.005577522998620441,
"Nucleotide GTR":0.005456007016996627,
"amino-acid": [
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]
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"Global MG94xREV":0.005616748937255812,
"Nucleotide GTR":0.005494378350740257,
"amino-acid": [
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],
"original name":"epi_isl_417356_Washington_20200313_null_2",
"synonymous substitution count": [
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]
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"epi_isl_417368_USA_20200313_null_1":{
"Global MG94xREV":0.005622229910074802,
"Nucleotide GTR":0.005499739911090214,
"amino-acid": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417368_USA_20200313_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417952_Madrid_20200309_null_1":{
"Global MG94xREV":0.02958254479133468,
"Nucleotide GTR":0.02893803790716069,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417952_Madrid_20200309_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418099_Wales_20200313_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_418099_Wales_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418305_South_Yorkshire_20200325_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_418305_South_Yorkshire_20200325_null_1",
"synonymous substitution count": [
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]
},
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"Global MG94xREV":0.005592052545918171,
"Nucleotide GTR":0.005470220012986029,
"amino-acid": [
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],
"original name":"epi_isl_418861_Barcelona_20200324_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005600120120647947,
"Nucleotide GTR":0.005478111821652113,
"amino-acid": [
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],
"original name":"epi_isl_419184_ARA_20200322_null_1",
"synonymous substitution count": [
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]
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"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_419546_Duesseldorf_20200315_null_1",
"synonymous substitution count": [
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]
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"epi_isl_419898_Victoria_20200319_null_1":{
"Global MG94xREV":0.005622217241140647,
"Nucleotide GTR":0.005499727518170698,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_419898_Victoria_20200319_null_1",
"synonymous substitution count": [
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]
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"epi_isl_420168_South_Yorkshire_20200325_null_1":{
"Global MG94xREV":0.005600102715407237,
"Nucleotide GTR":0.005478094795614664,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_420168_South_Yorkshire_20200325_null_1",
"synonymous substitution count": [
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]
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"epi_isl_420388_Vilvoorde_20200324_null_2":{
"Global MG94xREV":0.005616344757029816,
"Nucleotide GTR":0.005493982976279279,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_420388_Vilvoorde_20200324_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_421323_Wisconsin_20200322_null_2":{
"Global MG94xREV":0.005592034380587096,
"Nucleotide GTR":0.005470202243418099,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421323_Wisconsin_20200322_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_421808_England_20200325_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_421808_England_20200325_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422093_Wales_20200329_null_1":{
"Global MG94xREV":0.00561681734979539,
"Nucleotide GTR":0.005494445272794383,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422093_Wales_20200329_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422884_Noord_Brabant_20200101_null_1":{
"Global MG94xREV":0.00561680837223305,
"Nucleotide GTR":0.005494436490823758,
"amino-acid": [
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],
"codon": [
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],
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[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, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_422884_Noord_Brabant_20200101_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, 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_423125_England_20200324_null_1":{
"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", "IV", "D", "-", "-"]
],
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],
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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, 0, 0, 0, 0, 0, 1, 0, 0, 0]
],
"original name":"epi_isl_423125_England_20200324_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, 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_423144_England_20200324_null_1":{
"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", "QP", "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", "CMA", "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, 1, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423144_England_20200324_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, 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_423307_England_20200326_null_1":{
"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": [
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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, 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_423307_England_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, 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_423368_England_20200329_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "PL", "V", "D", "F", "Q", "V", "T", "I", "A", "-", "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": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423368_England_20200329_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423372_England_20200328_null_1":{
"Global MG94xREV":0.005600157464533115,
"Nucleotide GTR":0.005478148351936179,
"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": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423372_England_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, 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_423469_England_20200331_null_3":{
"Global MG94xREV":0.005616353770916384,
"Nucleotide GTR":0.005493991793782742,
"amino-acid": [
["M", "F", "Y", "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": [
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],
"nonsynonymous substitution count": [
[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, 0, 0, 0]
],
"original name":"epi_isl_423469_England_20200331_null_3",
"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, 0, 0]
]
},
"epi_isl_423491_England_20200331_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "TA", "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": [
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],
"nonsynonymous substitution count": [
[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, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423491_England_20200331_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, 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_423586_England_20200402_null_1":{
"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": [
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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, 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_423586_England_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, 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]
]
},
"epi_isl_423697_England_20200321_null_2":{
"Global MG94xREV":0.005616344741531929,
"Nucleotide GTR":0.005493982961119036,
"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", "TTA", "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, 0, 0]
],
"original name":"epi_isl_423697_England_20200321_null_2",
"synonymous substitution count": [
[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, 0, 0, 0]
]
},
"epi_isl_423802_England_20200223_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "ED", "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": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423802_England_20200223_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, 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_423875_England_20200318_null_1":{
"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", "RS", "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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],
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],
"original name":"epi_isl_423875_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, 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_423879_England_20200319_null_1":{
"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", "-", "-"]
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],
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],
"original name":"epi_isl_423879_England_20200319_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423953_England_20200318_null_7":{
"Global MG94xREV":0.005619148527414238,
"Nucleotide GTR":0.005496725661678379,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423953_England_20200318_null_7",
"synonymous substitution count": [
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]
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"epi_isl_423963_England_20200320_null_1":{
"Global MG94xREV":0.005648888484744401,
"Nucleotide GTR":0.005525817682620058,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423963_England_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424019_England_20200319_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_424019_England_20200319_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424174_Connecticut_20200313_null_1":{
"Global MG94xREV":0.005617890799459208,
"Nucleotide GTR":0.00549549533550137,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424174_Connecticut_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424360_Beijing_20200129_null_1":{
"Global MG94xREV":0.005622183203136841,
"Nucleotide GTR":0.005499694221743657,
"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": [
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],
"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, 0, 0]
],
"original name":"epi_isl_424360_Beijing_20200129_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424964_New_York_20200401_null_1":{
"Global MG94xREV":0.005674418603538054,
"Nucleotide GTR":0.005550791583636224,
"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", "D", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424964_New_York_20200401_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, 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_425023_England_20200324_null_4":{
"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": [
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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, 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_425023_England_20200324_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0]
]
},
"epi_isl_425293_England_20200319_null_3":{
"Global MG94xREV":0.005616371839855016,
"Nucleotide GTR":0.005494009469058312,
"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": [
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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, 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_425293_England_20200319_null_3",
"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, 0, 0]
]
},
"epi_isl_425305_England_20200328_null_2":{
"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", "-", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425305_England_20200328_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, 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_425575_England_20200324_null_1":{
"Global MG94xREV":0.005620920817630042,
"Nucleotide GTR":0.005498459339487683,
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_425575_England_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_426508_Arizona_20200301_null_3":{
"Global MG94xREV":0.00561524988791087,
"Nucleotide GTR":0.005492911960777033,
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_426508_Arizona_20200301_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_426642_Victoria_20200318_null_3":{
"Global MG94xREV":0.005600157256417298,
"Nucleotide GTR":0.005478148148354523,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_426642_Victoria_20200318_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_426852_Victoria_20200325_null_1":{
"Global MG94xREV":0.005592034338417287,
"Nucleotide GTR":0.005470202202167035,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_426852_Victoria_20200325_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_426880_Victoria_20200323_null_2":{
"Global MG94xREV":0.005622194845463415,
"Nucleotide GTR":0.005499705610422009,
"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, 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]
],
"original name":"epi_isl_426880_Victoria_20200323_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_426968_Victoria_20200327_null_15":{
"Global MG94xREV":0.005622218249981944,
"Nucleotide GTR":0.005499728505032641,
"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, 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]
],
"original name":"epi_isl_426968_Victoria_20200327_null_15",
"synonymous substitution count": [
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]
},
"epi_isl_426994_Victoria_20200329_null_3":{
"Global MG94xREV":0.005622218228786176,
"Nucleotide GTR":0.00549972848429866,
"amino-acid": [
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],
"codon": [
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],
"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, 0, 0]
],
"original name":"epi_isl_426994_Victoria_20200329_null_3",
"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, 0, 0]
]
},
"epi_isl_427005_Victoria_20200329_null_2":{
"Global MG94xREV":0.005622229880409804,
"Nucleotide GTR":0.005499739882071525,
"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", "Y", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_427005_Victoria_20200329_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, 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_427244_Washington_20200331_null_1":{
"Global MG94xREV":0.01128127791455581,
"Nucleotide GTR":0.01103549577074441,
"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", "I", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"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, 0, 0, 0, 0, 0, 0, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_427244_Washington_20200331_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, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_427427_Wisconsin_20200413_null_2":{
"Global MG94xREV":0.005600147978427491,
"Nucleotide GTR":0.005478139072501764,
"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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],
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],
"original name":"epi_isl_427427_Wisconsin_20200413_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, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_428445_Guangdong_20200130_null_1":{
"Global MG94xREV":0.005627222692769795,
"Nucleotide GTR":0.005504623917382073,
"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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"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, 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_428445_Guangdong_20200130_null_1",
"synonymous substitution count": [
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]
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"epi_isl_428906_Republic_of_Buryatia_20200327_null_1":{
"Global MG94xREV":0.005617753585581962,
"Nucleotide GTR":0.005495361111065663,
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_428906_Republic_of_Buryatia_20200327_null_1",
"synonymous substitution count": [
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]
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"epi_isl_429310_Unknown_20200317_null_3":{
"Global MG94xREV":0.01131928859730956,
"Nucleotide GTR":0.01107267832505688,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429310_Unknown_20200317_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_429398_Unknown_20200309_null_3":{
"Global MG94xREV":0.005616362922959447,
"Nucleotide GTR":0.00549400074643273,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429398_Unknown_20200309_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_429628_USA_20200406_null_1":{
"Global MG94xREV":0.005637050632626404,
"Nucleotide GTR":0.005514237738577166,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429628_USA_20200406_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_429646_Connecticut_20200406_null_8":{
"Global MG94xREV":0.005616362910938542,
"Nucleotide GTR":0.005494000734673719,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429646_Connecticut_20200406_null_8",
"synonymous 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, 0, 0]
]
},
"epi_isl_429691_Minas_gerais_20200318_null_1":{
"Global MG94xREV":0.005617926812261874,
"Nucleotide GTR":0.005495530563702855,
"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, 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]
],
"original name":"epi_isl_429691_Minas_gerais_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, 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_429724_Luxembourg_20200319_null_1":{
"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": [
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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, 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_429724_Luxembourg_20200319_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_429780_Luxembourg_20200326_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "T", "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": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429780_Luxembourg_20200326_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_429787_Luxembourg_20200322_null_17":{
"Global MG94xREV":0.00101688981690939,
"Nucleotide GTR":0.0009947351141254537,
"amino-acid": [
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"original name":"epi_isl_429787_Luxembourg_20200322_null_17",
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]
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"Global MG94xREV":0.005616353768038966,
"Nucleotide GTR":0.005493991790968022,
"amino-acid": [
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"original name":"epi_isl_430036_Utah_20200314_null_10",
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.005459565245032762,
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"original name":"epi_isl_430114_Washington_20200312_null_1",
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]
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"epi_isl_430204_Washington_20200318_null_39":{
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"Nucleotide GTR":0,
"amino-acid": [
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"synonymous substitution count": [
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"epi_isl_430262_Washington_20200319_null_11769":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430262_Washington_20200319_null_11769",
"synonymous substitution count": [
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"epi_isl_430289_Washington_20200311_null_14":{
"Global MG94xREV":0.005622205580016409,
"Nucleotide GTR":0.005499716111104211,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430289_Washington_20200311_null_14",
"synonymous substitution count": [
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]
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"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
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"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",
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}
}
},
"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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]
],
"name":"slac.filter.default"
}
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"fits":{
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"Equilibrium frequencies": [
[0.05253180703236421],
[0.01838906108577841],
[0.03165114539004305],
[0.06499740166426604],
[0.01796809896808336],
[0.006289836352209082],
[0.01082602988454429],
[0.0222318593581272],
[0.004417957576590104],
[0.001546531450940584],
[0.002661880972370624],
[0.005466321822213373],
[0.05390076910944453],
[0.01886827413177234],
[0.03247596410812808],
[0.06669121314751313],
[0.02091727041500314],
[0.007322210773603522],
[0.01260294675681395],
[0.02588085778291264],
[0.007154590831558221],
[0.002504505656243997],
[0.004310740623797779],
[0.008852347564129398],
[0.001759155424724177],
[0.0006158024707716872],
[0.001059915644579379],
[0.002176596203138911],
[0.02146236778689693],
[0.007513025242697963],
[0.01293137551539275],
[0.02655530465288779],
[0.02685766419086566],
[0.009401679769418064],
[0.0161821167434488],
[0.03323088402617064],
[0.009186456653503473],
[0.003215771969524198],
[0.005534968080961539],
[0.01136636728698998],
[0.002258746228326872],
[0.0007906871039936715],
[0.001360926061955948],
[0.0027947379721729],
[0.02755756632317954],
[0.009646684534954823],
[0.01660381752627204],
[0.03409687022747635],
[0.01228820856334116],
[0.04343351865547134],
[0.01200690707245084],
[0.004203086854989279],
[0.007234328741075752],
[0.01485609968171851],
[0.001033445967158255],
[0.00177876121062953],
[0.00365278587701519],
[0.03601836382247862],
[0.01260843534533828],
[0.02170156585998239],
[0.04456538224959573]
],
"Log Likelihood":-595.2527161250202,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.7280543855067498, 1]
]
},
"display order":1,
"estimated parameters":88
},
"Nucleotide GTR":{
"AIC-c":1487.541856322289,
"Equilibrium frequencies": [
[0.3602353930222782],
[0.1425809163514082],
[0.1407313997477932],
[0.3564522908785204]
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"Log Likelihood":-607.2596926685114,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.1205423132671004,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.3385381919612399,
"Substitution rate from nucleotide C to nucleotide G":0.9198530118763337,
"Substitution rate from nucleotide C to nucleotide T":2.731473572657004,
"Substitution rate from nucleotide G to nucleotide T":1.754974963331766
},
"display order":0,
"estimated parameters":135
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-26/sequences.ORF6.compressed.fas",
"number of sequences":65,
"number of sites":63,
"partition count":1,
"trees":{
"0":"(epi_isl_423372_England_20200328_null_1,epi_isl_424174_Connecticut_20200313_null_1,epi_isl_424964_New_York_20200401_null_1,epi_isl_425293_England_20200319_null_3,epi_isl_422093_Wales_20200329_null_1,epi_isl_420168_South_Yorkshire_20200325_null_1,epi_isl_427244_Washington_20200331_null_1,epi_isl_430262_Washington_20200319_null_11769,epi_isl_419898_Victoria_20200319_null_1,epi_isl_423697_England_20200321_null_2,epi_isl_420388_Vilvoorde_20200324_null_2,epi_isl_423963_England_20200320_null_1,epi_isl_430036_Utah_20200314_null_10,epi_isl_430289_Washington_20200311_null_14,epi_isl_429398_Unknown_20200309_null_3,epi_isl_429628_USA_20200406_null_1,(epi_isl_419546_Duesseldorf_20200315_null_1,epi_isl_429787_Luxembourg_20200322_null_17)Node90,(epi_isl_423491_England_20200331_null_2,epi_isl_429780_Luxembourg_20200326_null_1)Node82,epi_isl_418099_Wales_20200313_null_1,epi_isl_424019_England_20200319_null_1,epi_isl_423879_England_20200319_null_1,epi_isl_423802_England_20200223_null_1,epi_isl_423586_England_20200402_null_1,epi_isl_423307_England_20200326_null_1,epi_isl_423125_England_20200324_null_1,epi_isl_421808_England_20200325_null_1,epi_isl_423368_England_20200329_null_1,epi_isl_425575_England_20200324_null_1,(epi_isl_417952_Madrid_20200309_null_1,epi_isl_430097_St_Petersburg_20200414_null_1)Node59,epi_isl_426508_Arizona_20200301_null_3,epi_isl_424360_Beijing_20200129_null_1,epi_isl_426642_Victoria_20200318_null_3,((epi_isl_418305_South_Yorkshire_20200325_null_1,epi_isl_430114_Washington_20200312_null_1)Node75,epi_isl_414010_England_20200226_null_1)Node74,epi_isl_425023_England_20200324_null_4,(epi_isl_429310_Unknown_20200317_null_3,epi_isl_430204_Washington_20200318_null_39)Node67,(epi_isl_417356_Washington_20200313_null_2,epi_isl_429724_Luxembourg_20200319_null_1)Node70,epi_isl_429646_Connecticut_20200406_null_8,epi_isl_429691_Minas_gerais_20200318_null_1,epi_isl_423144_England_20200324_null_1,epi_isl_428906_Republic_of_Buryatia_20200327_null_1,epi_isl_419184_ARA_20200322_null_1,epi_isl_426994_Victoria_20200329_null_3,epi_isl_423875_England_20200318_null_1,epi_isl_423953_England_20200318_null_7,epi_isl_428445_Guangdong_20200130_null_1,(epi_isl_416636_Washington_20200312_null_1,epi_isl_425305_England_20200328_null_2)Node12,epi_isl_422884_Noord_Brabant_20200101_null_1,epi_isl_421323_Wisconsin_20200322_null_2,epi_isl_427005_Victoria_20200329_null_2,epi_isl_417368_USA_20200313_null_1,epi_isl_426852_Victoria_20200325_null_1,epi_isl_418861_Barcelona_20200324_null_1,epi_isl_426968_Victoria_20200327_null_15,epi_isl_415655_Wales_20200312_null_1,epi_isl_423469_England_20200331_null_3,epi_isl_426880_Victoria_20200323_null_2,epi_isl_427427_Wisconsin_20200413_null_2)"
}
},
"tested":{
"0":{
"Node12":"test",
"Node59":"test",
"Node67":"test",
"Node70":"test",
"Node74":"test",
"Node75":"test",
"Node82":"test",
"Node90":"test",
"epi_isl_414010_England_20200226_null_1":"test",
"epi_isl_415655_Wales_20200312_null_1":"test",
"epi_isl_416636_Washington_20200312_null_1":"test",
"epi_isl_417356_Washington_20200313_null_2":"test",
"epi_isl_417368_USA_20200313_null_1":"test",
"epi_isl_417952_Madrid_20200309_null_1":"test",
"epi_isl_418099_Wales_20200313_null_1":"test",
"epi_isl_418305_South_Yorkshire_20200325_null_1":"test",
"epi_isl_418861_Barcelona_20200324_null_1":"test",
"epi_isl_419184_ARA_20200322_null_1":"test",
"epi_isl_419546_Duesseldorf_20200315_null_1":"test",
"epi_isl_419898_Victoria_20200319_null_1":"test",
"epi_isl_420168_South_Yorkshire_20200325_null_1":"test",
"epi_isl_420388_Vilvoorde_20200324_null_2":"test",
"epi_isl_421323_Wisconsin_20200322_null_2":"test",
"epi_isl_421808_England_20200325_null_1":"test",
"epi_isl_422093_Wales_20200329_null_1":"test",
"epi_isl_422884_Noord_Brabant_20200101_null_1":"test",
"epi_isl_423125_England_20200324_null_1":"test",
"epi_isl_423144_England_20200324_null_1":"test",
"epi_isl_423307_England_20200326_null_1":"test",
"epi_isl_423368_England_20200329_null_1":"test",
"epi_isl_423372_England_20200328_null_1":"test",
"epi_isl_423469_England_20200331_null_3":"test",
"epi_isl_423491_England_20200331_null_2":"test",
"epi_isl_423586_England_20200402_null_1":"test",
"epi_isl_423697_England_20200321_null_2":"test",
"epi_isl_423802_England_20200223_null_1":"test",
"epi_isl_423875_England_20200318_null_1":"test",
"epi_isl_423879_England_20200319_null_1":"test",
"epi_isl_423953_England_20200318_null_7":"test",
"epi_isl_423963_England_20200320_null_1":"test",
"epi_isl_424019_England_20200319_null_1":"test",
"epi_isl_424174_Connecticut_20200313_null_1":"test",
"epi_isl_424360_Beijing_20200129_null_1":"test",
"epi_isl_424964_New_York_20200401_null_1":"test",
"epi_isl_425023_England_20200324_null_4":"test",
"epi_isl_425293_England_20200319_null_3":"test",
"epi_isl_425305_England_20200328_null_2":"test",
"epi_isl_425575_England_20200324_null_1":"test",
"epi_isl_426508_Arizona_20200301_null_3":"test",
"epi_isl_426642_Victoria_20200318_null_3":"test",
"epi_isl_426852_Victoria_20200325_null_1":"test",
"epi_isl_426880_Victoria_20200323_null_2":"test",
"epi_isl_426968_Victoria_20200327_null_15":"test",
"epi_isl_426994_Victoria_20200329_null_3":"test",
"epi_isl_427005_Victoria_20200329_null_2":"test",
"epi_isl_427244_Washington_20200331_null_1":"test",
"epi_isl_427427_Wisconsin_20200413_null_2":"test",
"epi_isl_428445_Guangdong_20200130_null_1":"test",
"epi_isl_428906_Republic_of_Buryatia_20200327_null_1":"test",
"epi_isl_429310_Unknown_20200317_null_3":"test",
"epi_isl_429398_Unknown_20200309_null_3":"test",
"epi_isl_429628_USA_20200406_null_1":"test",
"epi_isl_429646_Connecticut_20200406_null_8":"test",
"epi_isl_429691_Minas_gerais_20200318_null_1":"test",
"epi_isl_429724_Luxembourg_20200319_null_1":"test",
"epi_isl_429780_Luxembourg_20200326_null_1":"test",
"epi_isl_429787_Luxembourg_20200322_null_17":"test",
"epi_isl_430036_Utah_20200314_null_10":"test",
"epi_isl_430097_St_Petersburg_20200414_null_1":"test",
"epi_isl_430114_Washington_20200312_null_1":"test",
"epi_isl_430204_Washington_20200318_null_39":"test",
"epi_isl_430262_Washington_20200319_null_11769":"test",
"epi_isl_430289_Washington_20200311_null_14":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":2
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":4
}
}
}