{
"MLE":{
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"NAMES": [
["epi_isl_417222_England_20200304_null_1"],
["epi_isl_423309_England_20200325_null_1"],
["epi_isl_423534_England_20200331_null_3"],
["epi_isl_423904_England_20200318_null_1"],
["Node69"],
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["epi_isl_422359_Wales_20200324_null_1"],
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["epi_isl_422425_Zhejiang_20200124_null_1"],
["epi_isl_424315_Idaho_20200320_null_1"],
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["Node31"],
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["epi_isl_423043_Bangkok_20200318_null_2"],
["epi_isl_421562_Utah_20200319_null_1"],
["epi_isl_424158_England_20200321_null_1"],
["Node18"],
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["epi_isl_425251_England_20200331_null_1"],
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["epi_isl_424600_Reykjavik_20200327_null_1"],
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["epi_isl_423536_England_20200331_null_1"],
["epi_isl_421889_England_20200327_null_1"],
["epi_isl_422636_Prague_20200308_null_1"],
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["Node60"],
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[0.81212974421701, 2.190605290441729, 1.583333333333333, 4.166666666666666, 0.2704633392034567, 1.949606383226187, 1.902061811339125, -1.052560824288544e-05, 0.689465736535039, 0.6340286451666901, 4517.037950676073],
[0.0002643285395064849, 0.0008152846906675182, 0, 0, 0.2448363285283959, 0, 0, 0, 1, 1, 4520.416748428077]
]
}
}
},
"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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[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]
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"original name":"epi_isl_407073_England_20200129_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414480_USA_20200221_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "IM", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"original name":"epi_isl_414480_USA_20200221_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414934_Shandong_20200121_null_1":{
"Global MG94xREV":0.008887925136263032,
"Nucleotide GTR":0.008776428224265284,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_414934_Shandong_20200121_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414937_Shandong_20200126_null_1":{
"Global MG94xREV":1.130829170321746,
"Nucleotide GTR":1.116643186691731,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "N", "S", "G", "L", "N", "S", "C", "R", "P", "H", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_414937_Shandong_20200126_null_1",
"synonymous substitution count": [
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]
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"epi_isl_415435_Wales_20200306_null_1":{
"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_415435_Wales_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416373_Shanghai_20200207_null_1":{
"Global MG94xREV":0.008924928872723574,
"Nucleotide GTR":0.008812967757631816,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "I", "-"]
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"codon": [
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"original name":"epi_isl_416373_Shanghai_20200207_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416567_unknown_20200215_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_416567_unknown_20200215_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416604_unknown_20200216_null_1":{
"Global MG94xREV":0.02209062398801049,
"Nucleotide GTR":0.02181350235151998,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_416604_unknown_20200216_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416677_Washington_20200312_null_1":{
"Global MG94xREV":0.0089245464290519,
"Nucleotide GTR":0.008812590111625255,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "V", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416677_Washington_20200312_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417222_England_20200304_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417222_England_20200304_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418113_Wales_20200313_null_1":{
"Global MG94xREV":0.02712994884812567,
"Nucleotide GTR":0.02678961007694489,
"amino-acid": [
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],
"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418113_Wales_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418182_Madrid_20200312_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "Q", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418182_Madrid_20200312_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_418999_Singapore_20200301_null_4":{
"Global MG94xREV":0.0001968967302635311,
"Nucleotide GTR":0.000194426707500033,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "K", "KNTRSIM", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418999_Singapore_20200301_null_4",
"synonymous substitution count": [
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]
},
"epi_isl_419835_Northern_Territory_20200224_null_17":{
"Global MG94xREV":0.008928188168798002,
"Nucleotide GTR":0.008816186166610321,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_419835_Northern_Territory_20200224_null_17",
"synonymous substitution count": [
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]
},
"epi_isl_421291_Wisconsin_20200323_null_2":{
"Global MG94xREV":0.008872588293260148,
"Nucleotide GTR":0.008761283778318908,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421291_Wisconsin_20200323_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_421562_Utah_20200319_null_1":{
"Global MG94xREV":0.003281722756348996,
"Nucleotide GTR":0.003240554323024471,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
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],
"original name":"epi_isl_421562_Utah_20200319_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_421881_England_20200326_null_4":{
"Global MG94xREV":0.008924697961844289,
"Nucleotide GTR":0.0088127397434747,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "C", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_421881_England_20200326_null_4",
"synonymous substitution count": [
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]
},
"epi_isl_421889_England_20200327_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "YSCF", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421889_England_20200327_null_1",
"synonymous substitution count": [
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]
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"epi_isl_422051_Wales_20200330_null_1":{
"Global MG94xREV":0.008924428692669699,
"Nucleotide GTR":0.008812473852218027,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "M", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_422051_Wales_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422206_Wales_20200330_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422206_Wales_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422359_Wales_20200324_null_1":{
"Global MG94xREV":0.008923535747672771,
"Nucleotide GTR":0.008811592109004224,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "I", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422359_Wales_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422425_Zhejiang_20200124_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "EDAGV", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422425_Zhejiang_20200124_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422581_Netherlands_20200330_null_1":{
"Global MG94xREV":0.008925688723821759,
"Nucleotide GTR":0.008813718076578254,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "L", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422581_Netherlands_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422636_Prague_20200308_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "C", "K", "I", "N", "F", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422636_Prague_20200308_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422725_Netherlands_20200323_null_8":{
"Global MG94xREV":0.008869621661628834,
"Nucleotide GTR":0.008758354362377515,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "C", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422725_Netherlands_20200323_null_8",
"synonymous substitution count": [
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]
},
"epi_isl_422985_Washington_20200317_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "C", "K", "IM", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422985_Washington_20200317_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423043_Bangkok_20200318_null_2":{
"Global MG94xREV":0.008925755441674704,
"Nucleotide GTR":0.008813783957471557,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "F", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423043_Bangkok_20200318_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_423187_England_20200329_null_6":{
"Global MG94xREV":0.008923840201909726,
"Nucleotide GTR":0.008811892743935009,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "F", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423187_England_20200329_null_6",
"synonymous substitution count": [
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]
},
"epi_isl_423309_England_20200325_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "KQE", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423309_England_20200325_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423534_England_20200331_null_3":{
"Global MG94xREV":0.003060534018932572,
"Nucleotide GTR":0.003022140345837514,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423534_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]
]
},
"epi_isl_423536_England_20200331_null_1":{
"Global MG94xREV":0.008869633503317627,
"Nucleotide GTR":0.008758366055515129,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "---", "ACG", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTG", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423536_England_20200331_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_423770_England_20200322_null_1":{
"Global MG94xREV":0.008871448817363958,
"Nucleotide GTR":0.008760158596877479,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "T", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423770_England_20200322_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_423807_England_20200324_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "Y"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423807_England_20200324_null_2",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]
]
},
"epi_isl_423904_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "ILV", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423904_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_424158_England_20200321_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_424158_England_20200321_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, 3, 0, 0]
]
},
"epi_isl_424288_Washington_20200322_null_3":{
"Global MG94xREV":0.3295090024030481,
"Nucleotide GTR":0.325375390150454,
"amino-acid": [
["-", "-", "-", "V", "K", "L", "I", "-", "-", "-", "-", "-", "L", "V", "V", "-", "L", "S", "P", "C", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "GTA", "AAA", "TTA", "ATT", "---", "---", "---", "---", "---", "TTA", "GTA", "GTG", "---", "CTA", "TCC", "CCA", "TGT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 1, 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]
],
"original name":"epi_isl_424288_Washington_20200322_null_3",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_424315_Idaho_20200320_null_1":{
"Global MG94xREV":0.3241260368813838,
"Nucleotide GTR":0.3200599526540436,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "EDAGV", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "AAG", "GNN", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"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, 17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_424315_Idaho_20200320_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, 1, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_424366_Kayseri_20200317_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_424366_Kayseri_20200317_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_424479_Reykjavik_20200320_null_1":{
"Global MG94xREV":1.006437887535143,
"Nucleotide GTR":0.9938123630333835,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "Y", "G", "R", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424479_Reykjavik_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424600_Reykjavik_20200327_null_1":{
"Global MG94xREV":0.008872706850327754,
"Nucleotide GTR":0.008761400848116229,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "R", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424600_Reykjavik_20200327_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_425131_Duesseldorf_20200320_null_1":{
"Global MG94xREV":0.008922199846354674,
"Nucleotide GTR":0.008810272966251189,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "Y", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425131_Duesseldorf_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_425228_Prague_20200322_null_50":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_425228_Prague_20200322_null_50",
"synonymous substitution count": [
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]
},
"epi_isl_425251_England_20200331_null_1":{
"Global MG94xREV":0.008875327384107892,
"Nucleotide GTR":0.008763988507921872,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425251_England_20200331_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_425750_Scotland_20200319_null_2":{
"Global MG94xREV":0.00892220087306515,
"Nucleotide GTR":0.008810273980081849,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "V", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425750_Scotland_20200319_null_2",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_426014_Scotland_20200401_null_10":{
"Global MG94xREV":0.008925747837018118,
"Nucleotide GTR":0.008813776448213601,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "S", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426014_Scotland_20200401_null_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_426051_Prague_20200320_null_8538":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "---", "ACG", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426051_Prague_20200320_null_8538",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_426093_Washington_20200325_null_8":{
"Global MG94xREV":2.039784005361191,
"Nucleotide GTR":2.014195398993187,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "G", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TTA", "GGN", "---"]
],
"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, 8.666666666666666, 0]
],
"original name":"epi_isl_426093_Washington_20200325_null_8",
"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, 2.333333333333333, 0]
]
},
"epi_isl_426103_Washington_20200323_null_2":{
"Global MG94xREV":0.5564158007560142,
"Nucleotide GTR":0.5494356965562238,
"amino-acid": [
["L", "G", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["TTA", "GGA", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426103_Washington_20200323_null_2",
"synonymous substitution count": [
[0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_426167_South_Korea_20200223_null_4":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "---", "ACA", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426167_South_Korea_20200223_null_4",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_426360_Central_Czechia_and_Prague_20200318_null_10":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426360_Central_Czechia_and_Prague_20200318_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_426506_Arizona_20200317_null_8":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "---", "ACG", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGT", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_426506_Arizona_20200317_null_8",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
}
},
"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"amino-acid":{
"attribute type":"node label",
"display order":1
},
"codon":{
"attribute type":"node label",
"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
"attribute type":"branch label",
"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":1212.791079066774,
"Equilibrium frequencies": [
[0.03183687780234325],
[0.02303896026807938],
[0.01447058384231303],
[0.03701233768372704],
[0.01609183534952206],
[0.0116449595830288],
[0.007314104544033419],
[0.01870775292744344],
[0.0154304357687019],
[0.01116633354568796],
[0.007013483416957183],
[0.01793883504607414],
[0.04670397319089282],
[0.03379762894423106],
[0.02122801626540815],
[0.05429625472840272],
[0.01365107850474986],
[0.009878690279868341],
[0.006204725138796141],
[0.0158702222781306],
[0.006899888519397037],
[0.004993148462594066],
[0.003136155999417729],
[0.008021546756108036],
[0.006616292318260751],
[0.004787922257602437],
[0.003007255086728292],
[0.007691848648540911],
[0.02002582063702506],
[0.01449181320029273],
[0.009102190181408582],
[0.02328125390979035],
[0.01815313542610033],
[0.01313663256866875],
[0.008251012232264602],
[0.02110414163664632],
[0.0091754369937897],
[0.006639863671764561],
[0.004170444449132572],
[0.01066701246643319],
[0.008798312194180404],
[0.006366954898226898],
[0.003999032664797358],
[0.01022858158389798],
[0.02663023539980528],
[0.01927114018889621],
[0.01210404664948181],
[0.03095929416615687],
[0.01995444458382142],
[0.032057030032336],
[0.01393741874623169],
[0.01008590222720843],
[0.006334873280128201],
[0.01620311050215693],
[0.009671355883651237],
[0.006074500088318849],
[0.01553713733866519],
[0.04045112427114071],
[0.02927271482674593],
[0.01838595445556794],
[0.04702693148822747]
],
"Log Likelihood":-524.1710497374688,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.879142075119521, 1]
]
},
"display order":1,
"estimated parameters":79
},
"Nucleotide GTR":{
"AIC-c":1275.90108815397,
"Equilibrium frequencies": [
[0.3022388059701492],
[0.179982440737489],
[0.158252853380158],
[0.3595258999122037]
],
"Log Likelihood":-529.0283883883623,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.4925481881738899,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.08959267564594287,
"Substitution rate from nucleotide C to nucleotide G":0.2283407081900558,
"Substitution rate from nucleotide C to nucleotide T":1.419953038230418,
"Substitution rate from nucleotide G to nucleotide T":0.7044730876903167
},
"display order":0,
"estimated parameters":107
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-17/sequences.ORF10.compressed.fas",
"number of sequences":51,
"number of sites":40,
"partition count":1,
"trees":{
"0":"(epi_isl_417222_England_20200304_null_1,epi_isl_423309_England_20200325_null_1,(epi_isl_423534_England_20200331_null_3,epi_isl_423904_England_20200318_null_1)Node69,epi_isl_423770_England_20200322_null_1,epi_isl_422581_Netherlands_20200330_null_1,epi_isl_421881_England_20200326_null_4,epi_isl_422359_Wales_20200324_null_1,epi_isl_422725_Netherlands_20200323_null_8,((((epi_isl_422425_Zhejiang_20200124_null_1,epi_isl_424315_Idaho_20200320_null_1)Node33,epi_isl_418999_Singapore_20200301_null_4)Node32,epi_isl_426093_Washington_20200325_null_8)Node31,epi_isl_426103_Washington_20200323_null_2)Node30,epi_isl_423043_Bangkok_20200318_null_2,(epi_isl_421562_Utah_20200319_null_1,epi_isl_424158_England_20200321_null_1)Node18,epi_isl_421291_Wisconsin_20200323_null_2,epi_isl_425251_England_20200331_null_1,((epi_isl_415435_Wales_20200306_null_1,epi_isl_424288_Washington_20200322_null_3)Node47,epi_isl_426167_South_Korea_20200223_null_4)Node46,epi_isl_422051_Wales_20200330_null_1,epi_isl_424600_Reykjavik_20200327_null_1,epi_isl_425750_Scotland_20200319_null_2,epi_isl_423536_England_20200331_null_1,epi_isl_421889_England_20200327_null_1,((epi_isl_422636_Prague_20200308_null_1,epi_isl_422985_Washington_20200317_null_1)Node61,epi_isl_426506_Arizona_20200317_null_8)Node60,epi_isl_423187_England_20200329_null_6,epi_isl_425131_Duesseldorf_20200320_null_1,epi_isl_416373_Shanghai_20200207_null_1,epi_isl_423807_England_20200324_null_2,epi_isl_426051_Prague_20200320_null_8538,epi_isl_416677_Washington_20200312_null_1,epi_isl_407073_England_20200129_null_1,(epi_isl_416567_unknown_20200215_null_1,epi_isl_425228_Prague_20200322_null_50)Node78,epi_isl_418113_Wales_20200313_null_1,((epi_isl_418182_Madrid_20200312_null_3,epi_isl_424479_Reykjavik_20200320_null_1)Node10,epi_isl_424366_Kayseri_20200317_null_3)Node9,epi_isl_414934_Shandong_20200121_null_1,epi_isl_422206_Wales_20200330_null_1,epi_isl_426014_Scotland_20200401_null_10,epi_isl_419835_Northern_Territory_20200224_null_17,epi_isl_414480_USA_20200221_null_1,epi_isl_416604_unknown_20200216_null_1,epi_isl_414937_Shandong_20200126_null_1,epi_isl_426360_Central_Czechia_and_Prague_20200318_null_10)"
}
},
"tested":{
"0":{
"Node10":"test",
"Node18":"test",
"Node30":"test",
"Node31":"test",
"Node32":"test",
"Node33":"test",
"Node46":"test",
"Node47":"test",
"Node60":"test",
"Node61":"test",
"Node69":"test",
"Node78":"test",
"Node9":"test",
"epi_isl_407073_England_20200129_null_1":"test",
"epi_isl_414480_USA_20200221_null_1":"test",
"epi_isl_414934_Shandong_20200121_null_1":"test",
"epi_isl_414937_Shandong_20200126_null_1":"test",
"epi_isl_415435_Wales_20200306_null_1":"test",
"epi_isl_416373_Shanghai_20200207_null_1":"test",
"epi_isl_416567_unknown_20200215_null_1":"test",
"epi_isl_416604_unknown_20200216_null_1":"test",
"epi_isl_416677_Washington_20200312_null_1":"test",
"epi_isl_417222_England_20200304_null_1":"test",
"epi_isl_418113_Wales_20200313_null_1":"test",
"epi_isl_418182_Madrid_20200312_null_3":"test",
"epi_isl_418999_Singapore_20200301_null_4":"test",
"epi_isl_419835_Northern_Territory_20200224_null_17":"test",
"epi_isl_421291_Wisconsin_20200323_null_2":"test",
"epi_isl_421562_Utah_20200319_null_1":"test",
"epi_isl_421881_England_20200326_null_4":"test",
"epi_isl_421889_England_20200327_null_1":"test",
"epi_isl_422051_Wales_20200330_null_1":"test",
"epi_isl_422206_Wales_20200330_null_1":"test",
"epi_isl_422359_Wales_20200324_null_1":"test",
"epi_isl_422425_Zhejiang_20200124_null_1":"test",
"epi_isl_422581_Netherlands_20200330_null_1":"test",
"epi_isl_422636_Prague_20200308_null_1":"test",
"epi_isl_422725_Netherlands_20200323_null_8":"test",
"epi_isl_422985_Washington_20200317_null_1":"test",
"epi_isl_423043_Bangkok_20200318_null_2":"test",
"epi_isl_423187_England_20200329_null_6":"test",
"epi_isl_423309_England_20200325_null_1":"test",
"epi_isl_423534_England_20200331_null_3":"test",
"epi_isl_423536_England_20200331_null_1":"test",
"epi_isl_423770_England_20200322_null_1":"test",
"epi_isl_423807_England_20200324_null_2":"test",
"epi_isl_423904_England_20200318_null_1":"test",
"epi_isl_424158_England_20200321_null_1":"test",
"epi_isl_424288_Washington_20200322_null_3":"test",
"epi_isl_424315_Idaho_20200320_null_1":"test",
"epi_isl_424366_Kayseri_20200317_null_3":"test",
"epi_isl_424479_Reykjavik_20200320_null_1":"test",
"epi_isl_424600_Reykjavik_20200327_null_1":"test",
"epi_isl_425131_Duesseldorf_20200320_null_1":"test",
"epi_isl_425228_Prague_20200322_null_50":"test",
"epi_isl_425251_England_20200331_null_1":"test",
"epi_isl_425750_Scotland_20200319_null_2":"test",
"epi_isl_426014_Scotland_20200401_null_10":"test",
"epi_isl_426051_Prague_20200320_null_8538":"test",
"epi_isl_426093_Washington_20200325_null_8":"test",
"epi_isl_426103_Washington_20200323_null_2":"test",
"epi_isl_426167_South_Korea_20200223_null_4":"test",
"epi_isl_426360_Central_Czechia_and_Prague_20200318_null_10":"test",
"epi_isl_426506_Arizona_20200317_null_8":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":2
},
"Primary SLAC analysis":{
"order":2,
"timer":0
},
"Total time":{
"order":0,
"timer":2
}
}
}