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]
}
}
},
"headers": [
["ES", "Expected synonymous sites"],
["EN", "Expected non-synonymous sites"],
["S", "Inferred synonymous substitutions"],
["N", "Inferred non-synonymous substitutions"],
["P[S]", "Expected proportion of synonymous sites"],
["dS", "Inferred synonymous susbsitution rate"],
["dN", "Inferred non-synonymous susbsitution rate"],
["dN-dS", "Scaled by the length of the tested branches"],
["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"],
["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
]
},
"analysis":{
"authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
"citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
"contact":"spond@temple.edu",
"info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.00"
},
"branch attributes":{
"0":{
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"Global MG94xREV":110.3949716700284,
"Nucleotide GTR":100.3388060877941,
"amino-acid": [
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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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],
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],
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],
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],
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],
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]
},
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],
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"Nucleotide GTR":0.1516492925550239,
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"Nucleotide GTR":0.007811292655487766,
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"Nucleotide GTR":0.7096179028180228,
"amino-acid": [
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"Nucleotide GTR":0.4571566347216498,
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"Nucleotide GTR":0.97348597283217,
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"epi_isl_418638_Li_ge_20200319_null_1":{
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"Nucleotide GTR":0.00777386634955286,
"amino-acid": [
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"epi_isl_418991_Hangzhou_20200204_null_1":{
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"Nucleotide GTR":1.190027454323049e-05,
"amino-acid": [
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"original name":"epi_isl_418991_Hangzhou_20200204_null_1",
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"epi_isl_419575_Luxembourg_20200314_null_1":{
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"Nucleotide GTR":0,
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"epi_isl_420106_Singapore_20200306_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_420388_Vilvoorde_20200324_null_1":{
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"Nucleotide GTR":0.007811393151884672,
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"original name":"epi_isl_420388_Vilvoorde_20200324_null_1",
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"epi_isl_421952_England_20200331_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_421996_England_20200401_null_1":{
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"Nucleotide GTR":0.007805737031414046,
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"epi_isl_422349_Wales_20200324_null_2":{
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"Nucleotide GTR":0.007889244760694436,
"amino-acid": [
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"Nucleotide GTR":0.3283565151055996,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422998_Washington_20200317_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_423009_Washington_20200318_null_1":{
"Global MG94xREV":0.008046203555369424,
"Nucleotide GTR":0.007889379562944096,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "Y", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TA-", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 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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"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]
]
},
"epi_isl_423024_Washington_20200317_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "E", "A", "EDAGV", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "GAA", "GCT", "G??", "---", "---", "---"]
],
"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, 13, 0, 0, 0]
],
"original name":"epi_isl_423024_Washington_20200317_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423058_England_20200324_null_1":{
"Global MG94xREV":0.007927970393398072,
"Nucleotide GTR":0.007773450816511057,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "S", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TCT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423058_England_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423141_England_20200323_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "LF", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423141_England_20200323_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423152_England_20200324_null_1":{
"Global MG94xREV":0.003997970386684488,
"Nucleotide GTR":0.003920048212167831,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423152_England_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423428_England_20200330_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "KE", "T", "C", "H", "A", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423428_England_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423468_England_20200330_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423468_England_20200330_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_423531_England_20200326_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_423531_England_20200326_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423567_England_20200401_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["MI", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423567_England_20200401_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423669_England_20200320_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, 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_423669_England_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423823_England_20200322_null_1":{
"Global MG94xREV":0.007932859409427949,
"Nucleotide GTR":0.007778244543500888,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "C", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423823_England_20200322_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423881_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["ML", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423881_England_20200318_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423896_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423896_England_20200318_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424002_England_20200320_null_2":{
"Global MG94xREV":0.007969563935717249,
"Nucleotide GTR":0.007814233682674605,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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]
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"epi_isl_424220_Washington_20200321_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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]
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"Nucleotide GTR":0.007865144969281134,
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"original name":"epi_isl_424374_Reykjavik_20200301_null_1",
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"epi_isl_426930_Victoria_20200328_null_1":{
"Global MG94xREV":1.080185377598116e-05,
"Nucleotide GTR":1.059132096717426e-05,
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"original name":"epi_isl_426930_Victoria_20200328_null_1",
"synonymous substitution count": [
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"epi_isl_427266_Washington_20200330_null_1":{
"Global MG94xREV":0.007995071297458124,
"Nucleotide GTR":0.007839243894886914,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_427266_Washington_20200330_null_1",
"synonymous substitution count": [
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"epi_isl_428477_Guangdong_20200128_null_3":{
"Global MG94xREV":0.007960433333324966,
"Nucleotide GTR":0.007805281039677777,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_428477_Guangdong_20200128_null_3",
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"epi_isl_428830_Singapore_20200227_null_16":{
"Global MG94xREV":0.02257007666946298,
"Nucleotide GTR":0.02213017609917613,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_428830_Singapore_20200227_null_16",
"synonymous substitution count": [
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]
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"epi_isl_429103_Guangzhou_20200209_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429103_Guangzhou_20200209_null_1",
"synonymous substitution count": [
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"epi_isl_429783_Luxembourg_20200327_null_1":{
"Global MG94xREV":0.007927837048350107,
"Nucleotide GTR":0.007773320070415837,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_429783_Luxembourg_20200327_null_1",
"synonymous substitution count": [
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]
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"epi_isl_429845_Iowa_20200414_null_1":{
"Global MG94xREV":0.007928764932798385,
"Nucleotide GTR":0.007774229869994317,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_429845_Iowa_20200414_null_1",
"synonymous substitution count": [
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]
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"epi_isl_429990_California_20200321_null_1":{
"Global MG94xREV":0.006857652938211624,
"Nucleotide GTR":0.006723994312123309,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429990_California_20200321_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430137_Washington_20200321_null_1":{
"Global MG94xREV":0.007928079511900906,
"Nucleotide GTR":0.007773557808247008,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_430137_Washington_20200321_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_430628_Victoria_20200411_null_2":{
"Global MG94xREV":0.01605115964449174,
"Nucleotide GTR":0.01573831559062416,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_430628_Victoria_20200411_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_430715_Victoria_20200417_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_430715_Victoria_20200417_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430896_Washington_20200329_null_1":{
"Global MG94xREV":0.730463242108205,
"Nucleotide GTR":0.7162261971267975,
"amino-acid": [
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"codon": [
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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_430896_Washington_20200329_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_432041_Wales_20200401_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "TA", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
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"original name":"epi_isl_432041_Wales_20200401_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_432044_Wales_20200408_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_432044_Wales_20200408_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_432607_England_20200404_null_1":{
"Global MG94xREV":0.00792872860812475,
"Nucleotide GTR":0.007774194253304291,
"amino-acid": [
["V", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_432607_England_20200404_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_432900_England_20200302_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "V", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_432900_England_20200302_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_433307_Scotland_20200324_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_433307_Scotland_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_433953_England_20200413_null_1":{
"Global MG94xREV":0.007969874099765441,
"Nucleotide GTR":0.007814537801491158,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "Y", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_433953_England_20200413_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_435144_Madrid_20200311_null_1":{
"Global MG94xREV":0.007928197285518695,
"Nucleotide GTR":0.007773673286405971,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_435144_Madrid_20200311_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_435402_Iowa_20200426_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_435402_Iowa_20200426_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_435415_Baranya_20200330_null_1":{
"Global MG94xREV":0.007928270295567898,
"Nucleotide GTR":0.007773744873457693,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "P", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_435415_Baranya_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_435634_California_20200310_null_1":{
"Global MG94xREV":0.007999447436260423,
"Nucleotide GTR":0.007843534740848463,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "T", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "I", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"original name":"epi_isl_435634_California_20200310_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_436118_Victoria_20200411_null_10":{
"Global MG94xREV":0.007960502626088849,
"Nucleotide GTR":0.007805348981895692,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_436118_Victoria_20200411_null_10",
"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, 0, 0, 0, 0]
]
},
"epi_isl_436418_Tamil_Nadu_20200331_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "SL", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_436418_Tamil_Nadu_20200331_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_436725_Abruzzo_20200427_null_1":{
"Global MG94xREV":0.007930596514016527,
"Nucleotide GTR":0.007776025752901181,
"amino-acid": [
["K", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_436725_Abruzzo_20200427_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_437074_California_20200421_null_1":{
"Global MG94xREV":0.007928765642799084,
"Nucleotide GTR":0.007774230566156786,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAG", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"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]
],
"original name":"epi_isl_437074_California_20200421_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_437301_Styria_20200417_null_2":{
"Global MG94xREV":0.007969421825856852,
"Nucleotide GTR":0.00781409434259695,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "Y", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "TAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_437301_Styria_20200417_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]
]
},
"epi_isl_437384_Minnesota_20200416_null_8":{
"Global MG94xREV":0.007928853229771524,
"Nucleotide GTR":0.007774316446021191,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_437384_Minnesota_20200416_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_437476_Makkah_20200409_null_1":{
"Global MG94xREV":1.035595281317409,
"Nucleotide GTR":1.015411080726977,
"amino-acid": [
["M", "K", "D", "L", "S", "P", "R", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 1.5, 1, 0, 2.25, 1.5, 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]
],
"original name":"epi_isl_437476_Makkah_20200409_null_1",
"synonymous substitution count": [
[0, 0.5, 0, 1, 0.75, 0.5, 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]
]
},
"epi_isl_437478_Makkah_20200409_null_1":{
"Global MG94xREV":0.7013773531832398,
"Nucleotide GTR":0.6877072047752364,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "Y", "Q", "E", "YSCWLF", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TAC", "CAA", "GAG", "T??", "---", "---", "---", "---"]
],
"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, 2, 0, 23, 0, 0, 0, 0]
],
"original name":"epi_isl_437478_Makkah_20200409_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, 1, 0, 1, 8, 0, 0, 0, 0]
]
},
"epi_isl_437636_Unknown_20200331_null_2":{
"Global MG94xREV":0.007960571621537944,
"Nucleotide GTR":0.007805416632593589,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "V", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"original name":"epi_isl_437636_Unknown_20200331_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_437860_Washington_20200404_null_17":{
"Global MG94xREV":0.007928376337607968,
"Nucleotide GTR":0.007773848848692474,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_437860_Washington_20200404_null_17",
"synonymous substitution count": [
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]
},
"epi_isl_437867_Connecticut_20200402_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "I", "T", "QHPRL", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"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, 13, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_437867_Connecticut_20200402_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_438106_Vienna_20200325_null_6":{
"Global MG94xREV":0.003391578909023849,
"Nucleotide GTR":0.003325475567059091,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "L", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_438106_Vienna_20200325_null_6",
"synonymous substitution count": [
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]
},
"epi_isl_438536_England_20200401_null_2":{
"Global MG94xREV":0.007931366650625542,
"Nucleotide GTR":0.007776780879214107,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_438536_England_20200401_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_438844_Scotland_20200405_null_2":{
"Global MG94xREV":0.007993823687688443,
"Nucleotide GTR":0.007838020601572029,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "L", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_438844_Scotland_20200405_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]
]
},
"epi_isl_439249_Scotland_20200426_null_3":{
"Global MG94xREV":0.004142589509554004,
"Nucleotide GTR":0.004061848645692318,
"amino-acid": [
["M", "I", "E", "F", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_439249_Scotland_20200426_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_439286_Scotland_20200414_null_5":{
"Global MG94xREV":0.004169485703058352,
"Nucleotide GTR":0.00408822062073545,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_439286_Scotland_20200414_null_5",
"synonymous substitution count": [
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]
},
"epi_isl_439507_England_20200330_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "SF", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous 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]
],
"original name":"epi_isl_439507_England_20200330_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]
]
},
"epi_isl_439984_England_20200320_null_5":{
"Global MG94xREV":0.003987174472343126,
"Nucleotide GTR":0.00390946271487312,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAT", "GCC", "---"]
],
"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]
],
"original name":"epi_isl_439984_England_20200320_null_5",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0]
]
},
"epi_isl_440124_England_20200321_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "TI", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]
],
"original name":"epi_isl_440124_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, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_440219_England_20200309_null_2":{
"Global MG94xREV":0.007928072627388484,
"Nucleotide GTR":0.007773551057916714,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "P", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_440219_England_20200309_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]
]
},
"epi_isl_440525_England_20200310_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_440525_England_20200310_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, 1, 0, 0]
]
},
"epi_isl_440875_England_20200423_null_4":{
"Global MG94xREV":0.007969303222733449,
"Nucleotide GTR":0.007813978051099794,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_440875_England_20200423_null_4",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_441112_England_20200331_null_4":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "Y", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_441112_England_20200331_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]
]
},
"epi_isl_441633_England_20200407_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_441633_England_20200407_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_442014_England_20200409_null_1":{
"Global MG94xREV":0.01604524991420264,
"Nucleotide GTR":0.01573252104353814,
"amino-acid": [
["I", "N", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[1, 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]
],
"original name":"epi_isl_442014_England_20200409_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]
]
},
"epi_isl_442155_England_20200404_null_1":{
"Global MG94xREV":3.363865298338737e-06,
"Nucleotide GTR":3.298302106650101e-06,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "ATG", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"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]
],
"original name":"epi_isl_442155_England_20200404_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]
]
},
"epi_isl_442776_England_20200406_null_3":{
"Global MG94xREV":0.06340618897206329,
"Nucleotide GTR":0.06217037488525237,
"amino-acid": [
["-", "-", "M", "I", "E", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["---", "---", "ATG", "ATT", "GAA", "CTT", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 2.333333333333333, 1, 2, 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]
],
"original name":"epi_isl_442776_England_20200406_null_3",
"synonymous substitution count": [
[0, 0, 0.6666666666666666, 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]
]
},
"epi_isl_443051_England_20200412_null_3":{
"Global MG94xREV":0.007966925174614855,
"Nucleotide GTR":0.007811646352169065,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "T", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "ACC", "---"]
],
"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, 1, 0]
],
"original name":"epi_isl_443051_England_20200412_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]
]
},
"epi_isl_443306_Ile_de_France_20200402_null_1":{
"Global MG94xREV":0.004286165697304504,
"Nucleotide GTR":0.004202626471354988,
"amino-acid": [
["I", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATT", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_443306_Ile_de_France_20200402_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_443368_England_20200416_null_2":{
"Global MG94xREV":0.007964328809994247,
"Nucleotide GTR":0.007809100591819508,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "S", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]
],
"original name":"epi_isl_443368_England_20200416_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_443458_England_20200414_null_9":{
"Global MG94xREV":0.007960484101090999,
"Nucleotide GTR":0.007805330817958075,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "F", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_443458_England_20200414_null_9",
"synonymous substitution count": [
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]
},
"epi_isl_443634_England_20200413_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "LF", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
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[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]
],
"original name":"epi_isl_443634_England_20200413_null_1",
"synonymous substitution count": [
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]
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"epi_isl_443761_England_20200325_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "QE", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_443761_England_20200325_null_1",
"synonymous substitution count": [
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]
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"epi_isl_444068_California_20200430_null_2":{
"Global MG94xREV":0.007927872851314627,
"Nucleotide GTR":0.007773355175565063,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444068_California_20200430_null_2",
"synonymous substitution count": [
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]
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"epi_isl_444156_England_20200413_null_4":{
"Global MG94xREV":0.007960571304423193,
"Nucleotide GTR":0.007805416321659552,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444156_England_20200413_null_4",
"synonymous substitution count": [
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]
},
"epi_isl_445266_Antofagasta_20200312_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_445266_Antofagasta_20200312_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_445293_Punta_Arenas_20200320_null_1":{
"Global MG94xREV":0.007966862407415955,
"Nucleotide GTR":0.00781158480833005,
"amino-acid": [
["M", "I", "K", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_445293_Punta_Arenas_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_445592_Wales_20200406_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_445592_Wales_20200406_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_445622_Wales_20200407_null_2":{
"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_445622_Wales_20200407_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_446119_Wales_20200406_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "SL", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_446119_Wales_20200406_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_446934_Wales_20200416_null_3":{
"Global MG94xREV":0.007969356729588832,
"Nucleotide GTR":0.007814030515083389,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "S", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_446934_Wales_20200416_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_447224_Michigan_20200408_null_13":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "I", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_447224_Michigan_20200408_null_13",
"synonymous substitution count": [
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]
},
"epi_isl_447283_South_Coast_District_20200328_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_447283_South_Coast_District_20200328_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_447362_Jerusalem_District_20200401_null_7":{
"Global MG94xREV":0.003161163634941678,
"Nucleotide GTR":0.00309955118647081,
"amino-acid": [
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"codon": [
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"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "KNTRSIM", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"Global MG94xREV":0.007960791509411745,
"Nucleotide GTR":0.007805632234757493,
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"Nucleotide GTR":0.007773032431595916,
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"epi_isl_448089_England_20200506_null_31":{
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"Nucleotide GTR":0,
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"epi_isl_448251_England_20200411_null_1":{
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"Nucleotide GTR":0,
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"epi_isl_448303_England_20200415_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"synonymous substitution count": [
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"epi_isl_448536_England_20200404_null_4":{
"Global MG94xREV":0.003388446378117084,
"Nucleotide GTR":0.003322404090536521,
"amino-acid": [
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"original name":"epi_isl_448536_England_20200404_null_4",
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"epi_isl_448603_England_20200101_null_1":{
"Global MG94xREV":0.008612549206288936,
"Nucleotide GTR":0.008444686891820333,
"amino-acid": [
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"codon": [
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"epi_isl_448750_England_20200101_null_2":{
"Global MG94xREV":0.001840329195582007,
"Nucleotide GTR":0.001804460382440254,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_448750_England_20200101_null_2",
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"epi_isl_448914_England_20200415_null_1":{
"Global MG94xREV":0.01663577765310506,
"Nucleotide GTR":0.01631153914102827,
"amino-acid": [
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"original name":"epi_isl_448914_England_20200415_null_1",
"synonymous substitution count": [
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"epi_isl_449071_England_20200506_null_5":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_449071_England_20200506_null_5",
"synonymous substitution count": [
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"epi_isl_449351_England_20200326_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_449351_England_20200326_null_1",
"synonymous substitution count": [
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"epi_isl_449367_England_20200330_null_1":{
"Global MG94xREV":0.1708827267005279,
"Nucleotide GTR":0.1675521483410207,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_449367_England_20200330_null_1",
"synonymous substitution count": [
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"epi_isl_449375_England_20200328_null_6":{
"Global MG94xREV":0.3090322196335081,
"Nucleotide GTR":0.3030090478186903,
"amino-acid": [
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"Nucleotide GTR":0.00783783814990038,
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"Nucleotide GTR":0.007805794641065738,
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"epi_isl_450305_Quebec_20200327_null_3":{
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"Nucleotide GTR":0.004077546370964049,
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"epi_isl_450471_California_20200321_null_26201":{
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"Nucleotide GTR":0,
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"attributes":{
"Global MG94xREV":{
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"display order":1
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"Nucleotide GTR":{
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"amino-acid":{
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"codon":{
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"nonsynonymous substitution count":{
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"original name":{
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"display order":-1
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"synonymous substitution count":{
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}
}
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"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]
],
"name":"slac.filter.default"
}
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"fits":{
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"Equilibrium frequencies": [
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[0.01115512551992743],
[0.008339018072820182],
[0.02244538211151549],
[0.006089308486318614],
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[0.009545859996458335],
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[0.01732538243709361],
[0.04663316779420189],
[0.01563790730953004],
[0.01218353112739294],
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[0.04037261448837212],
[0.02218497605128327],
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[0.009435111167106446],
[0.007053220728087337],
[0.01898451747871581],
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[0.05916056820301253],
[0.04609214071606602],
[0.03445619628032173],
[0.09274263286968135]
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"Log Likelihood":-878.8164053023675,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *background*": [
[0.6691360062163931, 1]
],
"non-synonymous/synonymous rate ratio for *test*": [
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"display order":1,
"estimated parameters":168
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"Nucleotide GTR":{
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"Equilibrium frequencies": [
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[0.18657382263946],
[0.131332919543797],
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"Log Likelihood":-885.6732169732761,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.2340962281258225,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.1960260826521023,
"Substitution rate from nucleotide C to nucleotide G":0,
"Substitution rate from nucleotide C to nucleotide T":0.8596291580152392,
"Substitution rate from nucleotide G to nucleotide T":0.5244582853396722
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"display order":0,
"estimated parameters":241
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},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-21/sequences.ORF7b.compressed.fas",
"number of sequences":118,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_448303_England_20200415_null_1,epi_isl_423669_England_20200320_null_1,epi_isl_423141_England_20200323_null_1,epi_isl_430715_Victoria_20200417_null_1,epi_isl_423009_Washington_20200318_null_1,epi_isl_422349_Wales_20200324_null_2,epi_isl_445266_Antofagasta_20200312_null_1,epi_isl_420106_Singapore_20200306_null_1,epi_isl_439507_England_20200330_null_1,(epi_isl_438106_Vienna_20200325_null_6,epi_isl_445592_Wales_20200406_null_1)Node218,(epi_isl_436418_Tamil_Nadu_20200331_null_2,epi_isl_450305_Quebec_20200327_null_3)Node215,(epi_isl_421952_England_20200331_null_1,epi_isl_448536_England_20200404_null_4)Node212,(epi_isl_432044_Wales_20200408_null_1,epi_isl_439286_Scotland_20200414_null_5)Node209,((epi_isl_435634_California_20200310_null_1,epi_isl_447224_Michigan_20200408_null_13)Node205,epi_isl_440124_England_20200321_null_1)Node204,epi_isl_432041_Wales_20200401_null_1,epi_isl_446934_Wales_20200416_null_3,epi_isl_444156_England_20200413_null_4,epi_isl_440219_England_20200309_null_2,epi_isl_424374_Reykjavik_20200301_null_1,epi_isl_450471_California_20200321_null_26201,epi_isl_447866_Telangana_20200414_null_3,(epi_isl_419575_Luxembourg_20200314_null_1,epi_isl_423152_England_20200324_null_1)Node147,epi_isl_423058_England_20200324_null_1,epi_isl_429783_Luxembourg_20200327_null_1,epi_isl_447984_England_20200101_null_8,(epi_isl_442014_England_20200409_null_1,epi_isl_428830_Singapore_20200227_null_16,(epi_isl_437476_Makkah_20200409_null_1,epi_isl_449351_England_20200326_null_1)Node137,epi_isl_433307_Scotland_20200324_null_1)Node134,epi_isl_448603_England_20200101_null_1,epi_isl_435144_Madrid_20200311_null_1,(epi_isl_438536_England_20200401_null_2,epi_isl_447283_South_Coast_District_20200328_null_1)Node65,epi_isl_443051_England_20200412_null_3,epi_isl_428477_Guangdong_20200128_null_3,(epi_isl_439984_England_20200320_null_5,epi_isl_440525_England_20200310_null_2)Node169,((epi_isl_441112_England_20200331_null_4,epi_isl_449917_Washington_20200413_null_1,(epi_isl_418052_Washington_20200316_null_1,epi_isl_418991_Hangzhou_20200204_null_1)Node161,epi_isl_448914_England_20200415_null_1)Node158,epi_isl_423531_England_20200326_null_1)Node157,epi_isl_449918_Washington_20200413_null_25,epi_isl_430137_Washington_20200321_null_1,epi_isl_427266_Washington_20200330_null_1,epi_isl_443458_England_20200414_null_9,(epi_isl_439249_Scotland_20200426_null_3,epi_isl_443634_England_20200413_null_1)Node196,epi_isl_445622_Wales_20200407_null_2,epi_isl_433953_England_20200413_null_1,epi_isl_429845_Iowa_20200414_null_1,(epi_isl_423567_England_20200401_null_1,epi_isl_443306_Ile_de_France_20200402_null_1)Node181,(epi_isl_436725_Abruzzo_20200427_null_1,((epi_isl_422998_Washington_20200317_null_1,epi_isl_442155_England_20200404_null_1)Node187,epi_isl_448750_England_20200101_null_2)Node186,epi_isl_429103_Guangzhou_20200209_null_1)Node184,(epi_isl_446119_Wales_20200406_null_3,epi_isl_447362_Jerusalem_District_20200401_null_7)Node38,epi_isl_423881_England_20200318_null_1,((((((epi_isl_449506_England_20200331_null_5,epi_isl_449582_England_20200323_null_2)Node28,epi_isl_449433_England_20200327_null_2)Node27,epi_isl_424220_Washington_20200321_null_1)Node26,epi_isl_429990_California_20200321_null_1)Node25,epi_isl_442776_England_20200406_null_3)Node24,epi_isl_432900_England_20200302_null_2)Node23,epi_isl_432607_England_20200404_null_1,epi_isl_443761_England_20200325_null_1,epi_isl_445293_Punta_Arenas_20200320_null_1,epi_isl_421996_England_20200401_null_1,epi_isl_437301_Styria_20200417_null_2,epi_isl_437074_California_20200421_null_1,epi_isl_438844_Scotland_20200405_null_2,(epi_isl_449071_England_20200506_null_5,epi_isl_449375_England_20200328_null_6)Node50,epi_isl_441633_England_20200407_null_1,epi_isl_423428_England_20200330_null_1,epi_isl_420388_Vilvoorde_20200324_null_1,epi_isl_423468_England_20200330_null_2,epi_isl_437636_Unknown_20200331_null_2,epi_isl_417453_Washington_20200314_null_1,epi_isl_440875_England_20200423_null_4,epi_isl_418638_Li_ge_20200319_null_1,epi_isl_423823_England_20200322_null_1,epi_isl_444068_California_20200430_null_2,epi_isl_424002_England_20200320_null_2,epi_isl_437860_Washington_20200404_null_17,epi_isl_423896_England_20200318_null_1,((epi_isl_423024_Washington_20200317_null_1,epi_isl_437478_Makkah_20200409_null_1)Node79,epi_isl_448251_England_20200411_null_1)Node78,epi_isl_435402_Iowa_20200426_null_1,epi_isl_435415_Baranya_20200330_null_1,(epi_isl_443368_England_20200416_null_2,epi_isl_448089_England_20200506_null_31)Node89,epi_isl_436118_Victoria_20200411_null_10,epi_isl_430628_Victoria_20200411_null_2,(((epi_isl_418035_Connecticut_20200314_null_1,epi_isl_437867_Connecticut_20200402_null_1,epi_isl_430896_Washington_20200329_null_1,epi_isl_447772_Valle_del_Cauca_20200401_null_1)Node104,(epi_isl_413752_China_20200201_null_1,epi_isl_449367_England_20200330_null_1)Node101,epi_isl_413747_China_20200201_null_1,epi_isl_418065_Washington_20200313_null_1)Node96,epi_isl_426930_Victoria_20200328_null_1)Node95,epi_isl_437384_Minnesota_20200416_null_8)"
}
},
"tested":{
"0":{
"Node101":"test",
"Node104":"test",
"Node134":"test",
"Node137":"test",
"Node147":"test",
"Node157":"test",
"Node158":"test",
"Node161":"test",
"Node169":"test",
"Node181":"test",
"Node184":"test",
"Node186":"test",
"Node187":"test",
"Node196":"test",
"Node204":"test",
"Node205":"test",
"Node209":"test",
"Node212":"test",
"Node215":"test",
"Node218":"test",
"Node23":"test",
"Node24":"test",
"Node25":"test",
"Node26":"test",
"Node27":"test",
"Node28":"test",
"Node38":"test",
"Node50":"test",
"Node65":"test",
"Node78":"test",
"Node79":"test",
"Node89":"test",
"Node95":"test",
"Node96":"test",
"epi_isl_413747_China_20200201_null_1":"background",
"epi_isl_413752_China_20200201_null_1":"background",
"epi_isl_417453_Washington_20200314_null_1":"background",
"epi_isl_418035_Connecticut_20200314_null_1":"background",
"epi_isl_418052_Washington_20200316_null_1":"background",
"epi_isl_418065_Washington_20200313_null_1":"background",
"epi_isl_418638_Li_ge_20200319_null_1":"background",
"epi_isl_418991_Hangzhou_20200204_null_1":"background",
"epi_isl_419575_Luxembourg_20200314_null_1":"background",
"epi_isl_420106_Singapore_20200306_null_1":"background",
"epi_isl_420388_Vilvoorde_20200324_null_1":"background",
"epi_isl_421952_England_20200331_null_1":"background",
"epi_isl_421996_England_20200401_null_1":"background",
"epi_isl_422349_Wales_20200324_null_2":"background",
"epi_isl_422998_Washington_20200317_null_1":"background",
"epi_isl_423009_Washington_20200318_null_1":"background",
"epi_isl_423024_Washington_20200317_null_1":"background",
"epi_isl_423058_England_20200324_null_1":"background",
"epi_isl_423141_England_20200323_null_1":"background",
"epi_isl_423152_England_20200324_null_1":"background",
"epi_isl_423428_England_20200330_null_1":"background",
"epi_isl_423468_England_20200330_null_2":"background",
"epi_isl_423531_England_20200326_null_1":"background",
"epi_isl_423567_England_20200401_null_1":"background",
"epi_isl_423669_England_20200320_null_1":"background",
"epi_isl_423823_England_20200322_null_1":"background",
"epi_isl_423881_England_20200318_null_1":"background",
"epi_isl_423896_England_20200318_null_1":"background",
"epi_isl_424002_England_20200320_null_2":"background",
"epi_isl_424220_Washington_20200321_null_1":"background",
"epi_isl_424374_Reykjavik_20200301_null_1":"background",
"epi_isl_426930_Victoria_20200328_null_1":"background",
"epi_isl_427266_Washington_20200330_null_1":"background",
"epi_isl_428477_Guangdong_20200128_null_3":"background",
"epi_isl_428830_Singapore_20200227_null_16":"background",
"epi_isl_429103_Guangzhou_20200209_null_1":"background",
"epi_isl_429783_Luxembourg_20200327_null_1":"background",
"epi_isl_429845_Iowa_20200414_null_1":"background",
"epi_isl_429990_California_20200321_null_1":"background",
"epi_isl_430137_Washington_20200321_null_1":"background",
"epi_isl_430628_Victoria_20200411_null_2":"background",
"epi_isl_430715_Victoria_20200417_null_1":"background",
"epi_isl_430896_Washington_20200329_null_1":"background",
"epi_isl_432041_Wales_20200401_null_1":"background",
"epi_isl_432044_Wales_20200408_null_1":"background",
"epi_isl_432607_England_20200404_null_1":"background",
"epi_isl_432900_England_20200302_null_2":"background",
"epi_isl_433307_Scotland_20200324_null_1":"background",
"epi_isl_433953_England_20200413_null_1":"background",
"epi_isl_435144_Madrid_20200311_null_1":"background",
"epi_isl_435402_Iowa_20200426_null_1":"background",
"epi_isl_435415_Baranya_20200330_null_1":"background",
"epi_isl_435634_California_20200310_null_1":"background",
"epi_isl_436118_Victoria_20200411_null_10":"background",
"epi_isl_436418_Tamil_Nadu_20200331_null_2":"background",
"epi_isl_436725_Abruzzo_20200427_null_1":"background",
"epi_isl_437074_California_20200421_null_1":"background",
"epi_isl_437301_Styria_20200417_null_2":"background",
"epi_isl_437384_Minnesota_20200416_null_8":"background",
"epi_isl_437476_Makkah_20200409_null_1":"background",
"epi_isl_437478_Makkah_20200409_null_1":"background",
"epi_isl_437636_Unknown_20200331_null_2":"background",
"epi_isl_437860_Washington_20200404_null_17":"background",
"epi_isl_437867_Connecticut_20200402_null_1":"background",
"epi_isl_438106_Vienna_20200325_null_6":"background",
"epi_isl_438536_England_20200401_null_2":"background",
"epi_isl_438844_Scotland_20200405_null_2":"background",
"epi_isl_439249_Scotland_20200426_null_3":"background",
"epi_isl_439286_Scotland_20200414_null_5":"background",
"epi_isl_439507_England_20200330_null_1":"background",
"epi_isl_439984_England_20200320_null_5":"background",
"epi_isl_440124_England_20200321_null_1":"background",
"epi_isl_440219_England_20200309_null_2":"background",
"epi_isl_440525_England_20200310_null_2":"background",
"epi_isl_440875_England_20200423_null_4":"background",
"epi_isl_441112_England_20200331_null_4":"background",
"epi_isl_441633_England_20200407_null_1":"background",
"epi_isl_442014_England_20200409_null_1":"background",
"epi_isl_442155_England_20200404_null_1":"background",
"epi_isl_442776_England_20200406_null_3":"background",
"epi_isl_443051_England_20200412_null_3":"background",
"epi_isl_443306_Ile_de_France_20200402_null_1":"background",
"epi_isl_443368_England_20200416_null_2":"background",
"epi_isl_443458_England_20200414_null_9":"background",
"epi_isl_443634_England_20200413_null_1":"background",
"epi_isl_443761_England_20200325_null_1":"background",
"epi_isl_444068_California_20200430_null_2":"background",
"epi_isl_444156_England_20200413_null_4":"background",
"epi_isl_445266_Antofagasta_20200312_null_1":"background",
"epi_isl_445293_Punta_Arenas_20200320_null_1":"background",
"epi_isl_445592_Wales_20200406_null_1":"background",
"epi_isl_445622_Wales_20200407_null_2":"background",
"epi_isl_446119_Wales_20200406_null_3":"background",
"epi_isl_446934_Wales_20200416_null_3":"background",
"epi_isl_447224_Michigan_20200408_null_13":"background",
"epi_isl_447283_South_Coast_District_20200328_null_1":"background",
"epi_isl_447362_Jerusalem_District_20200401_null_7":"background",
"epi_isl_447772_Valle_del_Cauca_20200401_null_1":"background",
"epi_isl_447866_Telangana_20200414_null_3":"background",
"epi_isl_447984_England_20200101_null_8":"background",
"epi_isl_448089_England_20200506_null_31":"background",
"epi_isl_448251_England_20200411_null_1":"background",
"epi_isl_448303_England_20200415_null_1":"background",
"epi_isl_448536_England_20200404_null_4":"background",
"epi_isl_448603_England_20200101_null_1":"background",
"epi_isl_448750_England_20200101_null_2":"background",
"epi_isl_448914_England_20200415_null_1":"background",
"epi_isl_449071_England_20200506_null_5":"background",
"epi_isl_449351_England_20200326_null_1":"background",
"epi_isl_449367_England_20200330_null_1":"background",
"epi_isl_449375_England_20200328_null_6":"background",
"epi_isl_449433_England_20200327_null_2":"background",
"epi_isl_449506_England_20200331_null_5":"background",
"epi_isl_449582_England_20200323_null_2":"background",
"epi_isl_449917_Washington_20200413_null_1":"background",
"epi_isl_449918_Washington_20200413_null_25":"background",
"epi_isl_450305_Quebec_20200327_null_3":"background",
"epi_isl_450471_California_20200321_null_26201":"background"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":3
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":4
}
}
}