{
"MLE":{
"content":{
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"NAMES": [
["epi_isl_429612_Washington_20200326_null_10"],
["epi_isl_429646_Connecticut_20200406_null_8"],
["epi_isl_423372_England_20200328_null_1"],
["epi_isl_426968_Victoria_20200327_null_15"],
["epi_isl_422093_Wales_20200329_null_1"],
["epi_isl_419184_ARA_20200322_null_1"],
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["epi_isl_420168_South_Yorkshire_20200325_null_1"],
["epi_isl_424360_Beijing_20200129_null_1"],
["epi_isl_420388_Vilvoorde_20200324_null_2"],
["epi_isl_429691_Minas_gerais_20200318_null_1"],
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["epi_isl_425293_England_20200319_null_3"],
["epi_isl_423469_England_20200331_null_3"],
["epi_isl_424174_Connecticut_20200313_null_1"],
["epi_isl_414010_England_20200226_null_1"],
["epi_isl_418305_South_Yorkshire_20200325_null_1"],
["Node88"],
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["epi_isl_429780_Luxembourg_20200326_null_1"],
["Node80"],
["epi_isl_419546_Duesseldorf_20200315_null_1"],
["epi_isl_429787_Luxembourg_20200322_null_17"],
["Node56"],
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["epi_isl_423879_England_20200319_null_1"],
["epi_isl_423802_England_20200223_null_1"],
["epi_isl_423586_England_20200402_null_1"],
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["epi_isl_430097_St_Petersburg_20200414_null_1"],
["Node63"],
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["epi_isl_428786_New_York_20200406_null_36"],
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[0.5014575042186253, 2.498542495781375, 0, 0, 0.1671525014062084, 0, 0, 0, 1, 1, 0.3042628659831895],
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[0.5234801285075928, 2.448814336355302, 2, 5, 0.1761198746274756, 3.820584375765834, 2.041804446245508, -5.846194617842726, 0.8904807615855374, 0.3567805462643578, 0.3042628659831895],
[3.259583175801085, 11.42192249867734, 0, 0, 0.2220196789125912, 0, 0, 0, 1, 1, 0.05757935933969983],
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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":0.005465162659660587,
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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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]
},
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],
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]
},
"Node88":{
"Global MG94xREV":0.005591002103230338,
"Nucleotide GTR":0.005474159209494715,
"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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],
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]
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"Nucleotide GTR":0,
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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":0.005608497446415286,
"Nucleotide GTR":0.005491288928327011,
"amino-acid": [
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],
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],
"original name":"epi_isl_415655_Wales_20200312_null_1",
"synonymous substitution count": [
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"epi_isl_416636_Washington_20200312_null_1":{
"Global MG94xREV":0.005570052849965305,
"Nucleotide GTR":0.0054536477617121,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_416636_Washington_20200312_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417356_Washington_20200313_null_2":{
"Global MG94xREV":0.005607232867772597,
"Nucleotide GTR":0.005490050777330972,
"amino-acid": [
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"codon": [
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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":0.005608384663160771,
"Nucleotide GTR":0.005491178502059954,
"amino-acid": [
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"codon": [
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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":0.02950943023217946,
"Nucleotide GTR":0.0288927309075941,
"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": [
[0, 0, 0, 0, 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]
],
"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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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418305_South_Yorkshire_20200325_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418861_Barcelona_20200324_null_1":{
"Global MG94xREV":0.005585719071074258,
"Nucleotide GTR":0.005468986584158985,
"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", "S", "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_418861_Barcelona_20200324_null_1",
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]
},
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"Global MG94xREV":0.005589846589895639,
"Nucleotide GTR":0.005473027844518261,
"amino-acid": [
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],
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],
"original name":"epi_isl_419184_ARA_20200322_null_1",
"synonymous substitution count": [
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]
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"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":0.005608497224108527,
"Nucleotide GTR":0.005491288710666106,
"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":0.005589627037785281,
"Nucleotide GTR":0.005472812880691618,
"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":0.005608313216641036,
"Nucleotide GTR":0.005491108548656831,
"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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]
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"epi_isl_421323_Wisconsin_20200322_null_2":{
"Global MG94xREV":0.005585833283879463,
"Nucleotide GTR":0.005469098410101438,
"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":{
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"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":0.005604034419714854,
"Nucleotide GTR":0.005486919171660261,
"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":0.005604146875786613,
"Nucleotide GTR":0.005487029277582162,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422884_Noord_Brabant_20200101_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423125_England_20200324_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_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": [
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],
"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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],
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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":0.005589296933109841,
"Nucleotide GTR":0.00547248967466955,
"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", "-", "-"]
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"codon": [
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],
"nonsynonymous 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, 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_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":0.005607869846979754,
"Nucleotide GTR":0.005490674444703777,
"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": [
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],
"original name":"epi_isl_423469_England_20200331_null_3",
"synonymous substitution count": [
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]
},
"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": [
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],
"original name":"epi_isl_423491_England_20200331_null_2",
"synonymous substitution count": [
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]
},
"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":0.005607980816173859,
"Nucleotide GTR":0.005490783094821356,
"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_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": [
[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, 0, 0, 0]
],
"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", "-", "-"]
],
"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, 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]
],
"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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"Global MG94xREV":0.005607889345060456,
"Nucleotide GTR":0.005490693535306156,
"amino-acid": [
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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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"Global MG94xREV":0.005639028060419469,
"Nucleotide GTR":0.005521181501918779,
"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": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "QL", "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_424019_England_20200319_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424174_Connecticut_20200313_null_1":{
"Global MG94xREV":0.005602689032025615,
"Nucleotide GTR":0.005485601900395935,
"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":0.00560838479798552,
"Nucleotide GTR":0.005491178634067079,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"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":0.00565831436964984,
"Nucleotide GTR":0.005540064758505211,
"amino-acid": [
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],
"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": [
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]
},
"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": [
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],
"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":0.005608091676317616,
"Nucleotide GTR":0.00549089163816755,
"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": [
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],
"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", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425305_England_20200328_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_425575_England_20200324_null_1":{
"Global MG94xREV":0.005609424838692235,
"Nucleotide GTR":0.005492196939606554,
"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": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_426508_Arizona_20200301_null_3":{
"Global MG94xREV":0.005615209456508171,
"Nucleotide GTR":0.005497860668273769,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "Y", "-", "-"]
],
"codon": [
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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": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_426642_Victoria_20200318_null_3":{
"Global MG94xREV":0.005589627084108795,
"Nucleotide GTR":0.00547281292604704,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "T", "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, 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]
],
"original name":"epi_isl_426642_Victoria_20200318_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_426852_Victoria_20200325_null_1":{
"Global MG94xREV":0.005585833375325737,
"Nucleotide GTR":0.005469098499636627,
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426852_Victoria_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, 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_426880_Victoria_20200323_null_2":{
"Global MG94xREV":0.005608497232221578,
"Nucleotide GTR":0.005491288718609605,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"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":0.005608834724460975,
"Nucleotide GTR":0.005491619157807503,
"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":0.005608722472495117,
"Nucleotide GTR":0.005491509251726029,
"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":0.005608609767030109,
"Nucleotide GTR":0.005491398901622795,
"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":0.01127523190333222,
"Nucleotide GTR":0.01103959780790513,
"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, 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":0.005589407039729786,
"Nucleotide GTR":0.005472597480239373,
"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, 0, 0, 0]
],
"original name":"epi_isl_427427_Wisconsin_20200413_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_428445_Guangdong_20200130_null_1":{
"Global MG94xREV":0.005623884621187452,
"Nucleotide GTR":0.005506354536053843,
"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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],
"original name":"epi_isl_428445_Guangdong_20200130_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_428786_New_York_20200406_null_36":{
"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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],
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],
"original name":"epi_isl_428786_New_York_20200406_null_36",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005604406260222124,
"Nucleotide GTR":0.005487283241302833,
"amino-acid": [
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"codon": [
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],
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],
"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":0.01130168330590653,
"Nucleotide GTR":0.01106549641898284,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_429310_Unknown_20200317_null_3",
"synonymous substitution count": [
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]
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"epi_isl_429398_Unknown_20200309_null_3":{
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"Nucleotide GTR":0.0054907831195712,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_429398_Unknown_20200309_null_3",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005608610076905611,
"Nucleotide GTR":0.005491399205022404,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429612_Washington_20200326_null_10",
"synonymous substitution count": [
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"epi_isl_429628_USA_20200406_null_1":{
"Global MG94xREV":0.005626678073631781,
"Nucleotide GTR":0.005509089609863877,
"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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]
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"epi_isl_429646_Connecticut_20200406_null_8":{
"Global MG94xREV":0.005608091677727886,
"Nucleotide GTR":0.005490891639548359,
"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": [
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]
},
"epi_isl_429691_Minas_gerais_20200318_null_1":{
"Global MG94xREV":0.005602240331871931,
"Nucleotide GTR":0.005485162577349156,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429691_Minas_gerais_20200318_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_429724_Luxembourg_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_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": [
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],
"codon": [
["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "ACA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_429780_Luxembourg_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_429787_Luxembourg_20200322_null_17":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "T", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ACA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_429787_Luxembourg_20200322_null_17",
"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_430036_Utah_20200314_null_10":{
"Global MG94xREV":0.005608091647100518,
"Nucleotide GTR":0.005490891609561049,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAT", "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_430036_Utah_20200314_null_10",
"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, 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]
]
},
"epi_isl_430074_St_Petersburg_20200408_null_11599":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAT", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_430074_St_Petersburg_20200408_null_11599",
"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_430097_St_Petersburg_20200414_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", "T", "E", "I", "D", "-", "-"]
],
"codon": [
["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ACG", "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_430097_St_Petersburg_20200414_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]
]
}
},
"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, 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"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":1352.696204885704,
"Equilibrium frequencies": [
[0.05253154719583107],
[0.0183061404465119],
[0.03164667478762125],
[0.06508277570770928],
[0.01796947731667971],
[0.006261985284447408],
[0.01082538465171325],
[0.02226287867415121],
[0.004419411532577073],
[0.00154007206193064],
[0.002662394065850564],
[0.005475330251792082],
[0.05390387426210341],
[0.01878436759485914],
[0.03247340825897078],
[0.06678298937777055],
[0.02091605777975789],
[0.007288806664616805],
[0.01260049843815801],
[0.02591347808764905],
[0.007154760251522714],
[0.002493283617503844],
[0.004310255131440478],
[0.008864228859591646],
[0.001759641051943854],
[0.0006131979344192725],
[0.001060063734772964],
[0.002180067597910537],
[0.02146246605712832],
[0.007479218468582739],
[0.01292967216286755],
[0.0265904383003069],
[0.02685079785062551],
[0.009356938883259447],
[0.01617577461023918],
[0.03326619045829259],
[0.009184858026604223],
[0.003200730037314276],
[0.005533250598061279],
[0.01137937271529813],
[0.002258923104579096],
[0.000787187239243876],
[0.001360847122860522],
[0.002798641837222548],
[0.02755224447857377],
[0.009601378294858806],
[0.01659834836830495],
[0.03413523193897657],
[0.01223402656795712],
[0.04349493599980678],
[0.01200903399309662],
[0.004184896022289802],
[0.007234624022708741],
[0.01487832183821516],
[0.001029232927458394],
[0.001779282740190791],
[0.003659173049856461],
[0.0360240560682494],
[0.01255362663087007],
[0.02170203711444077],
[0.04463119185185324]
],
"Log Likelihood":-588.4515244960837,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.7635684172937178, 1]
]
},
"display order":1,
"estimated parameters":86
},
"Nucleotide GTR":{
"AIC-c":1469.886641480611,
"Equilibrium frequencies": [
[0.360228825136612],
[0.1424180327868853],
[0.1407103825136612],
[0.3566427595628415]
],
"Log Likelihood":-600.4534361056288,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.1210986773593722,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.3396910728012386,
"Substitution rate from nucleotide C to nucleotide G":0.9242378151112124,
"Substitution rate from nucleotide C to nucleotide T":2.617567399719773,
"Substitution rate from nucleotide G to nucleotide T":1.764299344695323
},
"display order":0,
"estimated parameters":133
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-25/sequences.ORF6.compressed.fas",
"number of sequences":64,
"number of sites":63,
"partition count":1,
"trees":{
"0":"(epi_isl_429612_Washington_20200326_null_10,epi_isl_429646_Connecticut_20200406_null_8,epi_isl_423372_England_20200328_null_1,epi_isl_426968_Victoria_20200327_null_15,epi_isl_422093_Wales_20200329_null_1,epi_isl_419184_ARA_20200322_null_1,epi_isl_427244_Washington_20200331_null_1,epi_isl_430074_St_Petersburg_20200408_null_11599,epi_isl_420168_South_Yorkshire_20200325_null_1,epi_isl_424360_Beijing_20200129_null_1,epi_isl_420388_Vilvoorde_20200324_null_2,epi_isl_429691_Minas_gerais_20200318_null_1,epi_isl_415655_Wales_20200312_null_1,epi_isl_425293_England_20200319_null_3,epi_isl_423469_England_20200331_null_3,epi_isl_424174_Connecticut_20200313_null_1,(epi_isl_414010_England_20200226_null_1,epi_isl_418305_South_Yorkshire_20200325_null_1)Node88,(epi_isl_423491_England_20200331_null_2,epi_isl_429780_Luxembourg_20200326_null_1)Node80,(epi_isl_419546_Duesseldorf_20200315_null_1,epi_isl_429787_Luxembourg_20200322_null_17)Node56,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_423697_England_20200321_null_2,epi_isl_423963_England_20200320_null_1,epi_isl_425575_England_20200324_null_1,(epi_isl_417952_Madrid_20200309_null_1,epi_isl_430097_St_Petersburg_20200414_null_1)Node63,epi_isl_426508_Arizona_20200301_null_3,epi_isl_425023_England_20200324_null_4,(epi_isl_428786_New_York_20200406_null_36,epi_isl_429310_Unknown_20200317_null_3)Node69,(epi_isl_417356_Washington_20200313_null_2,epi_isl_429724_Luxembourg_20200319_null_1)Node72,epi_isl_426994_Victoria_20200329_null_3,epi_isl_429398_Unknown_20200309_null_3,epi_isl_423144_England_20200324_null_1,epi_isl_428906_Republic_of_Buryatia_20200327_null_1,epi_isl_418861_Barcelona_20200324_null_1,epi_isl_426880_Victoria_20200323_null_2,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_424964_New_York_20200401_null_1,epi_isl_417368_USA_20200313_null_1,epi_isl_426852_Victoria_20200325_null_1,epi_isl_419898_Victoria_20200319_null_1,epi_isl_426642_Victoria_20200318_null_3,epi_isl_429628_USA_20200406_null_1,epi_isl_430036_Utah_20200314_null_10,epi_isl_427005_Victoria_20200329_null_2,epi_isl_427427_Wisconsin_20200413_null_2)"
}
},
"tested":{
"0":{
"Node12":"test",
"Node56":"test",
"Node63":"test",
"Node69":"test",
"Node72":"test",
"Node80":"test",
"Node88":"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_428786_New_York_20200406_null_36":"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_429612_Washington_20200326_null_10":"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_430074_St_Petersburg_20200408_null_11599":"test",
"epi_isl_430097_St_Petersburg_20200414_null_1":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}