{
"MLE":{
"content":{
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"NAMES": [
["epi_isl_413879_Guangdong_20200205_null_1"],
["epi_isl_416395_Shanghai_20200209_null_3"],
["Node40"],
["epi_isl_418315_Derbyshire_20200325_null_2536"],
["epi_isl_418041_Washington_20200314_null_1"],
["epi_isl_414686_Guangdong_20200227_null_1"],
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["epi_isl_418241_Boufarik_20200302_null_4"],
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["epi_isl_411929_South_Korea_20200101_null_1"],
["epi_isl_413015_Ontario_20200123_null_1"],
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["epi_isl_416374_Shanghai_20200207_null_1"],
["epi_isl_418343_Ontario_20200310_null_1"],
["epi_isl_416496_Hauts_de_France_20200310_null_1"],
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["epi_isl_418260_Abruzzo_20200316_null_1"],
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[0.9999999999999999, 2, 0, 1, 0.3333333333333334, 0, 0.5000000000000001, 5.630990000682753, 0.6666666666666666, 1, 0.08879433277973775],
[0.7406282980889634, 2.252676714051009, 0, 2, 0.2474282757972178, 0, 0.8878326781313338, 9.998753865673859, 0.5663642000695485, 1, 0.08879433277973775],
[0.9933479280389883, 2.006652071961011, 0, 1, 0.3311159760129961, 0, 0.4983424949312437, 5.612323211746257, 0.6688840239870039, 1, 0.08879433277973775],
[1.831223517428526, 1.163783066238107, 1, 0, 0.6114255399020369, 0.5460829824882536, 0, -6.149975627868741, 1, 0.6114255399020369, 0.08879433277973775],
[0.9999999999999999, 2, 0, 0, 0.3333333333333334, 0, 0, 0, 1, 1, 0.08879433277973775],
[0, 0, 0, 0, null, null, null, null, 1, 1, 0.08879433277973775]
]
}
}
},
"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":{
"Node24":{
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
],
"codon": [
["ATG", "TAC", "TCA", "TTC", "GTT", "TCG", "GAA", "GAG", "ACA", "GGT", "ACG", "TTA", "ATA", "GTT", "AAT", "AGC", "GTA", "CTT", "CTT", "TTT", "CTT", "GCT", "TTC", "GTG", "GTA", "TTC", "TTG", "CTA", "GTT", "ACA", "CTA", "GCC", "ATC", "CTT", "ACT", "GCG", "CTT", "CGA", "TTG", "TGT", "GCG", "TAC", "TGC", "TGC", "AAT", "ATT", "GTT", "AAC", "GTG", "AGT", "CTT", "GTA", "AAA", "CCT", "TCT", "TTT", "TAC", "GTT", "TAC", "TCT", "CGT", "GTT", "AAA", "AAT", "CTG", "AAT", "TCT", "TCT", "AGA", "GTT", "CCT", "GAT", "CTT", "CTG", "GTC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"synonymous substitution count": [
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]
},
"Node40":{
"Global MG94xREV":0.004439509490986945,
"Nucleotide GTR":0.004457512831089742,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
],
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],
"nonsynonymous substitution count": [
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],
"synonymous substitution count": [
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]
},
"epi_isl_411929_South_Korea_20200101_null_1":{
"Global MG94xREV":0.004438180385926035,
"Nucleotide GTR":0.004456178336169769,
"amino-acid": [
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],
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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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_411929_South_Korea_20200101_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_413015_Ontario_20200123_null_1":{
"Global MG94xREV":0.004441706114839405,
"Nucleotide GTR":0.004459718362810597,
"amino-acid": [
["M", "Y", "S", "F", "V", "L", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
],
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],
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],
"original name":"epi_isl_413015_Ontario_20200123_null_1",
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]
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"Global MG94xREV":0.004453537273018737,
"Nucleotide GTR":0.004471597499345406,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
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"Nucleotide GTR":0,
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"synonymous substitution count": [
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"Global MG94xREV":0.004425812596443764,
"Nucleotide GTR":0.004443760392155601,
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"Global MG94xREV":0.004469524459997427,
"Nucleotide GTR":0.004487649518433372,
"amino-acid": [
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"epi_isl_414688_Guangdong_20200225_null_2":{
"Global MG94xREV":0.004437902479156039,
"Nucleotide GTR":0.004455899302417137,
"amino-acid": [
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"epi_isl_416354_Shanghai_20200204_null_1":{
"Global MG94xREV":0.004440619822571876,
"Nucleotide GTR":0.004458627665351644,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_416354_Shanghai_20200204_null_1",
"synonymous substitution count": [
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"epi_isl_416374_Shanghai_20200207_null_1":{
"Global MG94xREV":0.004430201294935814,
"Nucleotide GTR":0.004448166887936231,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_416374_Shanghai_20200207_null_1",
"synonymous substitution count": [
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"epi_isl_416395_Shanghai_20200209_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_416395_Shanghai_20200209_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_416397_Shanghai_20200202_null_4":{
"Global MG94xREV":0.004440669959319528,
"Nucleotide GTR":0.004458678005416559,
"amino-acid": [
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],
"original name":"epi_isl_416397_Shanghai_20200202_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
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"Global MG94xREV":0.00443977600607164,
"Nucleotide GTR":0.00445778042696088,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "F", "R", "V", "P", "D", "L", "L", "V", "-"]
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],
"original name":"epi_isl_416412_Victoria_20200302_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
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"epi_isl_416496_Hauts_de_France_20200310_null_1":{
"Global MG94xREV":0.0044340325475275,
"Nucleotide GTR":0.004452013677231588,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "G", "L", "L", "V", "-"]
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"codon": [
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"original name":"epi_isl_416496_Hauts_de_France_20200310_null_1",
"synonymous substitution count": [
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"epi_isl_417285_England_20200306_null_1":{
"Global MG94xREV":0.00442556110409729,
"Nucleotide GTR":0.004443507879943697,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "L", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
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"codon": [
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"original name":"epi_isl_417285_England_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417287_England_20200306_null_1":{
"Global MG94xREV":0.004440874035870933,
"Nucleotide GTR":0.004458882909550282,
"amino-acid": [
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"original name":"epi_isl_417287_England_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417413_Turkey_20200317_null_1":{
"Global MG94xREV":0.004450871126730004,
"Nucleotide GTR":0.004468920541155386,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "KQE", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "H", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_417413_Turkey_20200317_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_417969_Madrid_20200309_null_1":{
"Global MG94xREV":0.004440874205306251,
"Nucleotide GTR":0.004458883079672697,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "L", "D", "L", "L", "V", "-"]
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417969_Madrid_20200309_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418041_Washington_20200314_null_1":{
"Global MG94xREV":0.004434044017020368,
"Nucleotide GTR":0.004452025193236175,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418041_Washington_20200314_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418241_Boufarik_20200302_null_4":{
"Global MG94xREV":0.00444087412270251,
"Nucleotide GTR":0.004458882996733978,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "F", "L", "V", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418241_Boufarik_20200302_null_4",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_418260_Abruzzo_20200316_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "IM", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_418260_Abruzzo_20200316_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 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_418303_Derbyshire_20200325_null_1":{
"Global MG94xREV":0.004431098793647273,
"Nucleotide GTR":0.00444906802623323,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "G", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
],
"codon": [
["ATG", "TAC", "TCA", "TTC", "GTT", "TCG", "GAA", "GAG", "ACA", "GGT", "ACG", "TTA", "ATA", "GTT", "AAT", "AGC", "GTA", "CTT", "CTT", "TTT", "CTT", "GCT", "TTC", "GTG", "GTA", "TTC", "TTG", "CTA", "GTT", "ACA", "CTA", "GCC", "ATC", "CTT", "ACT", "GCG", "CTT", "CGA", "TTG", "TGT", "GCG", "TAC", "TGC", "TGC", "AAT", "ATT", "GTT", "AAC", "GTG", "GGT", "CTT", "GTA", "AAA", "CCT", "TCT", "TTT", "TAC", "GTT", "TAC", "TCT", "CGT", "GTT", "AAA", "AAT", "CTG", "AAT", "TCT", "TCT", "AGA", "GTT", "CCT", "GAT", "CTT", "CTG", "GTC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_418303_Derbyshire_20200325_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_418315_Derbyshire_20200325_null_2536":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_418315_Derbyshire_20200325_null_2536",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_418343_Ontario_20200310_null_1":{
"Global MG94xREV":0.004438662943568397,
"Nucleotide GTR":0.004456662850706103,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
],
"codon": [
["ATG", "TAC", "TCA", "TTC", "GTT", "TCG", "GAA", "GAG", "ACA", "GGT", "ACG", "TTA", "ATA", "GTT", "AAT", "AGC", "GTA", "CTT", "CTT", "TTT", "CTT", "GCT", "TTC", "GTG", "GTA", "TTC", "TTG", "CTA", "GTT", "ACA", "CTA", "GCC", "ATC", "CTT", "ACT", "GCG", "CTT", "CGA", "TTG", "TGT", "GCG", "TAC", "TGC", "TGC", "AAT", "ATT", "GTT", "AAC", "GTG", "AGT", "CTT", "GTA", "AAA", "CCT", "TCT", "TTT", "TAC", "GTT", "TAC", "TCT", "CGT", "GTT", "AAA", "AAT", "CTG", "AAT", "TCT", "TCT", "AGA", "GTT", "CCT", "GAT", "CTT", "TTG", "GTC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_418343_Ontario_20200310_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0]
]
}
},
"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"amino-acid":{
"attribute type":"node label",
"display order":1
},
"codon":{
"attribute type":"node label",
"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
"attribute type":"branch label",
"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":939.3621584155187,
"Equilibrium frequencies": [
[0.01054187321148182],
[0.008785262706572736],
[0.008143057874472708],
[0.02158209103030757],
[0.01047061112562205],
[0.008725875144918653],
[0.008088011557962307],
[0.02143619809523034],
[0.006449285300575151],
[0.005374629773907743],
[0.004981743035418991],
[0.01320344683009827],
[0.02393279593185232],
[0.01994483289128491],
[0.01848686077525156],
[0.04899696382692568],
[0.008773196806500452],
[0.007311303899730495],
[0.006776845813480457],
[0.01796112780966385],
[0.008713890809212557],
[0.007261880163000103],
[0.006731034963878067],
[0.01783971225035733],
[0.005367248122619276],
[0.004472894316089165],
[0.004145924658014385],
[0.01098822147077731],
[0.01991744015771935],
[0.0165985627713132],
[0.01538520381169121],
[0.04077643488506531],
[0.01228217388460974],
[0.01023557407867328],
[0.009487351133931529],
[0.02514496138494665],
[0.01219914752749549],
[0.01016638254656265],
[0.009423217519579991],
[0.0249749837764887],
[0.007513962832226788],
[0.006261898253209655],
[0.005804151973941157],
[0.01538313225649877],
[0.02788373140930352],
[0.0232374171796562],
[0.02153875635450699],
[0.05708560684307875],
[0.01162613553040647],
[0.02856104862523933],
[0.01385647169567153],
[0.01154754393176319],
[0.01070341567293293],
[0.02836797858364938],
[0.00711261305031436],
[0.006592679313289944],
[0.01747301901403502],
[0.03167189626749631],
[0.02639435359763391],
[0.02446491995555562],
[0.06484101398630666]
],
"Log Likelihood":-429.7677302616235,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.8834735733715426, 1]
]
},
"display order":1,
"estimated parameters":39
},
"Nucleotide GTR":{
"AIC-c":975.9745924674879,
"Equilibrium frequencies": [
[0.2086473429951691],
[0.1982125603864734],
[0.1868115942028986],
[0.4063285024154589]
],
"Log Likelihood":-436.4765104093988,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.4538357089626803,
"Substitution rate from nucleotide C to nucleotide G":0.6925801487183896,
"Substitution rate from nucleotide C to nucleotide T":1.755122987633941,
"Substitution rate from nucleotide G to nucleotide T":0.1680343366751277
},
"display order":0,
"estimated parameters":51
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-03-30/sequences.E.compressed.fas",
"number of sequences":23,
"number of sites":76,
"partition count":1,
"trees":{
"0":"((epi_isl_413879_Guangdong_20200205_null_1,epi_isl_416395_Shanghai_20200209_null_3)Node40,epi_isl_418315_Derbyshire_20200325_null_2536,epi_isl_418041_Washington_20200314_null_1,epi_isl_414686_Guangdong_20200227_null_1,epi_isl_418303_Derbyshire_20200325_null_1,epi_isl_418241_Boufarik_20200302_null_4,epi_isl_414543_Noord_Brabant_20200301_null_1,epi_isl_417285_England_20200306_null_1,epi_isl_417287_England_20200306_null_1,epi_isl_411929_South_Korea_20200101_null_1,epi_isl_413015_Ontario_20200123_null_1,epi_isl_417969_Madrid_20200309_null_1,epi_isl_416374_Shanghai_20200207_null_1,epi_isl_418343_Ontario_20200310_null_1,epi_isl_416496_Hauts_de_France_20200310_null_1,epi_isl_414688_Guangdong_20200225_null_2,epi_isl_416412_Victoria_20200302_null_1,epi_isl_416397_Shanghai_20200202_null_4,epi_isl_416354_Shanghai_20200204_null_1,epi_isl_414010_England_20200226_null_1,epi_isl_418260_Abruzzo_20200316_null_1,epi_isl_417413_Turkey_20200317_null_1)"
}
},
"tested":{
"0":{
"Node40":"test",
"epi_isl_411929_South_Korea_20200101_null_1":"test",
"epi_isl_413015_Ontario_20200123_null_1":"test",
"epi_isl_413879_Guangdong_20200205_null_1":"test",
"epi_isl_414010_England_20200226_null_1":"test",
"epi_isl_414543_Noord_Brabant_20200301_null_1":"test",
"epi_isl_414686_Guangdong_20200227_null_1":"test",
"epi_isl_414688_Guangdong_20200225_null_2":"test",
"epi_isl_416354_Shanghai_20200204_null_1":"test",
"epi_isl_416374_Shanghai_20200207_null_1":"test",
"epi_isl_416395_Shanghai_20200209_null_3":"test",
"epi_isl_416397_Shanghai_20200202_null_4":"test",
"epi_isl_416412_Victoria_20200302_null_1":"test",
"epi_isl_416496_Hauts_de_France_20200310_null_1":"test",
"epi_isl_417285_England_20200306_null_1":"test",
"epi_isl_417287_England_20200306_null_1":"test",
"epi_isl_417413_Turkey_20200317_null_1":"test",
"epi_isl_417969_Madrid_20200309_null_1":"test",
"epi_isl_418041_Washington_20200314_null_1":"test",
"epi_isl_418241_Boufarik_20200302_null_4":"test",
"epi_isl_418260_Abruzzo_20200316_null_1":"test",
"epi_isl_418303_Derbyshire_20200325_null_1":"test",
"epi_isl_418315_Derbyshire_20200325_null_2536":"test",
"epi_isl_418343_Ontario_20200310_null_1":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}