{
"MLE":{
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"NAMES": [
["epi_isl_421728_New_York_20200318_null_4"],
["epi_isl_422956_Zuid_Holland_20200327_null_1"],
["epi_isl_422839_Netherlands_20200310_null_1"],
["epi_isl_419558_Oregon_20200227_null_5"],
["epi_isl_420073_Dakar_20200319_null_1"],
["epi_isl_421875_England_20200326_null_1"],
["epi_isl_422421_Taipei_20200319_null_4"],
["epi_isl_413879_Guangdong_20200205_null_1"],
["epi_isl_413878_Guangdong_20200209_null_4"],
["Node35"],
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["epi_isl_414688_Guangdong_20200225_null_2"],
["epi_isl_419754_Victoria_20200311_null_2"],
["epi_isl_422213_Wales_20200328_null_1"],
["Node40"],
["epi_isl_418653_Li_ge_20200322_null_1"],
["epi_isl_419999_Victoria_20200323_null_1"],
["epi_isl_420160_South_Yorkshire_20200327_null_1"],
["epi_isl_422937_Zuid_Holland_20200324_null_1"],
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["epi_isl_411929_South_Korea_20200101_null_1"],
["epi_isl_421509_Hauts_de_France_20200323_null_4"],
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["epi_isl_413015_Ontario_20200123_null_1"],
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["epi_isl_422718_Netherlands_20200323_null_1"],
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["Node76"],
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[1.928967229427578, 1.068707955479968, 1, 0, 0.6434877398123008, 0.5184121247600202, 0, -3.1845078772698, 1, 0.6434877398123008, 0.1627919115729978],
[1, 2.000000000000001, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1627919115729978],
[0, 0, 0, 0, null, null, null, null, 1, 1, 0.1627919115729978]
]
}
}
},
"headers": [
["ES", "Expected synonymous sites"],
["EN", "Expected non-synonymous sites"],
["S", "Inferred synonymous substitutions"],
["N", "Inferred non-synonymous substitutions"],
["P[S]", "Expected proportion of synonymous sites"],
["dS", "Inferred synonymous susbsitution rate"],
["dN", "Inferred non-synonymous susbsitution rate"],
["dN-dS", "Scaled by the length of the tested branches"],
["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"],
["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
]
},
"analysis":{
"authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
"citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
"contact":"spond@temple.edu",
"info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.00"
},
"branch attributes":{
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]
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"Global MG94xREV":0.004401522066883994,
"Nucleotide GTR":0.004460411080243287,
"amino-acid": [
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]
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"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", "VF", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "-"]
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"synonymous substitution count": [
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"Global MG94xREV":0.004392201356589973,
"Nucleotide GTR":0.004450965665943537,
"amino-acid": [
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"epi_isl_414686_Guangdong_20200227_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
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"synonymous substitution count": [
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]
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"epi_isl_414688_Guangdong_20200225_null_2":{
"Global MG94xREV":0.004400728079567199,
"Nucleotide GTR":0.004459606469980837,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_414688_Guangdong_20200225_null_2",
"synonymous substitution count": [
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]
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"epi_isl_416374_Shanghai_20200207_null_1":{
"Global MG94xREV":0.004400725646279074,
"Nucleotide GTR":0.00445960400413717,
"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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]
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"epi_isl_417413_Turkey_20200317_null_1":{
"Global MG94xREV":0.004429218936224356,
"Nucleotide GTR":0.0044884785126034,
"amino-acid": [
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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":0.004398041984613205,
"Nucleotide GTR":0.004456884437121902,
"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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"original name":"epi_isl_417969_Madrid_20200309_null_1",
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]
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"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", "-"]
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]
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"Global MG94xREV":0.004390951378644487,
"Nucleotide GTR":0.004449698964245044,
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"Global MG94xREV":0.004397758421979173,
"Nucleotide GTR":0.004456597080635768,
"amino-acid": [
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"epi_isl_419558_Oregon_20200227_null_5":{
"Global MG94xREV":0.004395306462804084,
"Nucleotide GTR":0.00445411231611416,
"amino-acid": [
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"original name":"epi_isl_419558_Oregon_20200227_null_5",
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"epi_isl_419754_Victoria_20200311_null_2":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_419754_Victoria_20200311_null_2",
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]
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"epi_isl_419999_Victoria_20200323_null_1":{
"Global MG94xREV":0.004398496097736384,
"Nucleotide GTR":0.004457344625932849,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_419999_Victoria_20200323_null_1",
"synonymous substitution count": [
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]
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"epi_isl_420057_Hauts_de_France_20200322_null_1":{
"Global MG94xREV":0.004400434405522772,
"Nucleotide GTR":0.004459308866801339,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_420057_Hauts_de_France_20200322_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_420073_Dakar_20200319_null_1":{
"Global MG94xREV":0.004401623484745727,
"Nucleotide GTR":0.004460513854998779,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_420073_Dakar_20200319_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_420160_South_Yorkshire_20200327_null_1":{
"Global MG94xREV":0.004402270173814258,
"Nucleotide GTR":0.004461169196274572,
"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", "M", "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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],
"original name":"epi_isl_420160_South_Yorkshire_20200327_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_420269_South_Yorkshire_20200323_null_5":{
"Global MG94xREV":0.004395306197155402,
"Nucleotide GTR":0.004454112046911303,
"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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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_420269_South_Yorkshire_20200323_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, 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]
]
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"epi_isl_420640_England_20200323_null_2":{
"Global MG94xREV":0.00443859655973531,
"Nucleotide GTR":0.004497981601575575,
"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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],
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],
"original name":"epi_isl_420640_England_20200323_null_2",
"synonymous substitution count": [
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]
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"epi_isl_420928_Wales_20200320_null_1":{
"Global MG94xREV":0.004400434317295269,
"Nucleotide GTR":0.004459308777393421,
"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", "H", "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_420928_Wales_20200320_null_1",
"synonymous substitution count": [
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]
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"epi_isl_421001_Wales_20200323_null_1":{
"Global MG94xREV":0.004401673502444686,
"Nucleotide GTR":0.004460564541896454,
"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", "S", "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_421001_Wales_20200323_null_1",
"synonymous substitution count": [
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]
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"epi_isl_421509_Hauts_de_France_20200323_null_4":{
"Global MG94xREV":0.00439185477580997,
"Nucleotide GTR":0.004450614448176637,
"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", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421509_Hauts_de_France_20200323_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_421513_Ile_de_France_20200323_null_6":{
"Global MG94xREV":0.004397523658902765,
"Nucleotide GTR":0.004456359176608182,
"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": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_421513_Ile_de_France_20200323_null_6",
"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_421728_New_York_20200318_null_4":{
"Global MG94xREV":0.004392536127810019,
"Nucleotide GTR":0.004451304916147573,
"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": [
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],
"original name":"epi_isl_421728_New_York_20200318_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_421864_England_20200327_null_1":{
"Global MG94xREV":0.00438873193088786,
"Nucleotide GTR":0.004447449821967609,
"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", "H", "L", "L", "V", "-"]
],
"codon": [
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"nonsynonymous substitution count": [
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]
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"Global MG94xREV":0.004400848210116604,
"Nucleotide GTR":0.004459728207785511,
"amino-acid": [
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.002078539694326112,
"amino-acid": [
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"original name":"epi_isl_421944_England_20200331_null_2",
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"Global MG94xREV":0.004397547011335427,
"Nucleotide GTR":0.004456382841478606,
"amino-acid": [
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"original name":"epi_isl_422209_Wales_20200327_null_5",
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"Global MG94xREV":0.004407016821759522,
"Nucleotide GTR":0.004465979350754622,
"amino-acid": [
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"original name":"epi_isl_422213_Wales_20200328_null_1",
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"epi_isl_422334_Wales_20200327_null_2":{
"Global MG94xREV":0.004397890412183077,
"Nucleotide GTR":0.004456730836768085,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_422334_Wales_20200327_null_2",
"synonymous substitution count": [
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]
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"epi_isl_422421_Taipei_20200319_null_4":{
"Global MG94xREV":0.004398066939002464,
"Nucleotide GTR":0.004456909725381886,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_422421_Taipei_20200319_null_4",
"synonymous substitution count": [
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]
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"epi_isl_422718_Netherlands_20200323_null_1":{
"Global MG94xREV":0.004398088266015746,
"Nucleotide GTR":0.00445693133773437,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_422718_Netherlands_20200323_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422839_Netherlands_20200310_null_1":{
"Global MG94xREV":0.004398113360351575,
"Nucleotide GTR":0.004456956767813301,
"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", "F", "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, 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_422839_Netherlands_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, 0, 0, 0]
]
},
"epi_isl_422854_Netherlands_20200318_null_1":{
"Global MG94xREV":0.002031453430594392,
"Nucleotide GTR":0.002058632730480929,
"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", "F", "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_422854_Netherlands_20200318_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_422884_Noord_Brabant_20200101_null_6041":{
"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_422884_Noord_Brabant_20200101_null_6041",
"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_422937_Zuid_Holland_20200324_null_1":{
"Global MG94xREV":0.004396999587444575,
"Nucleotide GTR":0.004455828093472972,
"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", "L", "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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_422937_Zuid_Holland_20200324_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_422956_Zuid_Holland_20200327_null_1":{
"Global MG94xREV":0.004401722404370229,
"Nucleotide GTR":0.004460614098092523,
"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_422956_Zuid_Holland_20200327_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
}
},
"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"amino-acid":{
"attribute type":"node label",
"display order":1
},
"codon":{
"attribute type":"node label",
"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
"attribute type":"branch label",
"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":1225.715636279726,
"Equilibrium frequencies": [
[0.01060883248636839],
[0.008844164321125388],
[0.008155588163905259],
[0.02173473985746964],
[0.01053841440046591],
[0.008785459546240795],
[0.00810145394049764],
[0.02159047150557344],
[0.006420253846177826],
[0.005352311865786798],
[0.004935599307881925],
[0.01315343110044356],
[0.02404940626079768],
[0.02004903942722228],
[0.01848809030602878],
[0.04927098146536692],
[0.008807885751480945],
[0.007342786212138844],
[0.006771102180763888],
[0.01804506817774107],
[0.008749421782305832],
[0.007294047111873636],
[0.006726157738891314],
[0.0179252907033876],
[0.005330356798950475],
[0.004443707776583411],
[0.004097736002031437],
[0.01092051538390746],
[0.01996679870364964],
[0.01664553087522272],
[0.01534956720146192],
[0.04090677990890255],
[0.01225787230910581],
[0.01021890364169711],
[0.00942329501830292],
[0.02511319376442496],
[0.01217650841667436],
[0.01015107378055124],
[0.009360746156405452],
[0.02494650030045886],
[0.007418219859689139],
[0.006184276685830239],
[0.005702790213971792],
[0.01519800402759038],
[0.02778765254644735],
[0.02316546759833387],
[0.02136188411889006],
[0.05692967629782355],
[0.01165550677573073],
[0.02864367943417485],
[0.01388831731186774],
[0.01157814119583069],
[0.01067670702037852],
[0.02845355171922125],
[0.007053680252015478],
[0.006504505014442066],
[0.01733458354557338],
[0.03169412139431624],
[0.0264221362704336],
[0.02436499979059865],
[0.06493301542857502]
],
"Log Likelihood":-550.6194422394046,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.8358947288757937, 1]
]
},
"display order":1,
"estimated parameters":61
},
"Nucleotide GTR":{
"AIC-c":1290.713925199092,
"Equilibrium frequencies": [
[0.2091327913279133],
[0.1985094850948509],
[0.1857723577235772],
[0.4065853658536585]
],
"Log Likelihood":-557.5301807420946,
"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":0.3226256353634682,
"Substitution rate from nucleotide C to nucleotide G":0.1473824097843375,
"Substitution rate from nucleotide C to nucleotide T":1.089659186586898,
"Substitution rate from nucleotide G to nucleotide T":0.5825165745309568
},
"display order":0,
"estimated parameters":87
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-11/sequences.E.compressed.fas",
"number of sequences":41,
"number of sites":76,
"partition count":1,
"trees":{
"0":"(epi_isl_421728_New_York_20200318_null_4,epi_isl_422956_Zuid_Holland_20200327_null_1,epi_isl_422839_Netherlands_20200310_null_1,epi_isl_419558_Oregon_20200227_null_5,epi_isl_420073_Dakar_20200319_null_1,epi_isl_421875_England_20200326_null_1,epi_isl_422421_Taipei_20200319_null_4,(epi_isl_413879_Guangdong_20200205_null_1,epi_isl_413878_Guangdong_20200209_null_4)Node35,epi_isl_422884_Noord_Brabant_20200101_null_6041,(epi_isl_414688_Guangdong_20200225_null_2,epi_isl_419754_Victoria_20200311_null_2,epi_isl_422213_Wales_20200328_null_1)Node40,epi_isl_418653_Li_ge_20200322_null_1,epi_isl_419999_Victoria_20200323_null_1,epi_isl_420160_South_Yorkshire_20200327_null_1,epi_isl_422937_Zuid_Holland_20200324_null_1,epi_isl_420057_Hauts_de_France_20200322_null_1,epi_isl_411929_South_Korea_20200101_null_1,epi_isl_421509_Hauts_de_France_20200323_null_4,epi_isl_416374_Shanghai_20200207_null_1,epi_isl_420269_South_Yorkshire_20200323_null_5,(epi_isl_414686_Guangdong_20200227_null_1,epi_isl_421864_England_20200327_null_1)Node53,epi_isl_417969_Madrid_20200309_null_1,epi_isl_420928_Wales_20200320_null_1,epi_isl_413015_Ontario_20200123_null_1,epi_isl_421001_Wales_20200323_null_1,epi_isl_421513_Ile_de_France_20200323_null_6,epi_isl_414543_Noord_Brabant_20200301_null_1,epi_isl_420640_England_20200323_null_2,epi_isl_422209_Wales_20200327_null_5,(epi_isl_421943_England_20200331_null_1,epi_isl_421944_England_20200331_null_2)Node71,epi_isl_417413_Turkey_20200317_null_1,epi_isl_418260_Abruzzo_20200316_null_1,epi_isl_422334_Wales_20200327_null_2,epi_isl_422718_Netherlands_20200323_null_1,(epi_isl_414010_England_20200226_null_1,epi_isl_422854_Netherlands_20200318_null_1)Node76,epi_isl_418303_Derbyshire_20200325_null_1)"
}
},
"tested":{
"0":{
"Node35":"test",
"Node40":"test",
"Node53":"test",
"Node71":"test",
"Node76":"test",
"epi_isl_411929_South_Korea_20200101_null_1":"test",
"epi_isl_413015_Ontario_20200123_null_1":"test",
"epi_isl_413878_Guangdong_20200209_null_4":"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_416374_Shanghai_20200207_null_1":"test",
"epi_isl_417413_Turkey_20200317_null_1":"test",
"epi_isl_417969_Madrid_20200309_null_1":"test",
"epi_isl_418260_Abruzzo_20200316_null_1":"test",
"epi_isl_418303_Derbyshire_20200325_null_1":"test",
"epi_isl_418653_Li_ge_20200322_null_1":"test",
"epi_isl_419558_Oregon_20200227_null_5":"test",
"epi_isl_419754_Victoria_20200311_null_2":"test",
"epi_isl_419999_Victoria_20200323_null_1":"test",
"epi_isl_420057_Hauts_de_France_20200322_null_1":"test",
"epi_isl_420073_Dakar_20200319_null_1":"test",
"epi_isl_420160_South_Yorkshire_20200327_null_1":"test",
"epi_isl_420269_South_Yorkshire_20200323_null_5":"test",
"epi_isl_420640_England_20200323_null_2":"test",
"epi_isl_420928_Wales_20200320_null_1":"test",
"epi_isl_421001_Wales_20200323_null_1":"test",
"epi_isl_421509_Hauts_de_France_20200323_null_4":"test",
"epi_isl_421513_Ile_de_France_20200323_null_6":"test",
"epi_isl_421728_New_York_20200318_null_4":"test",
"epi_isl_421864_England_20200327_null_1":"test",
"epi_isl_421875_England_20200326_null_1":"test",
"epi_isl_421943_England_20200331_null_1":"test",
"epi_isl_421944_England_20200331_null_2":"test",
"epi_isl_422209_Wales_20200327_null_5":"test",
"epi_isl_422213_Wales_20200328_null_1":"test",
"epi_isl_422334_Wales_20200327_null_2":"test",
"epi_isl_422421_Taipei_20200319_null_4":"test",
"epi_isl_422718_Netherlands_20200323_null_1":"test",
"epi_isl_422839_Netherlands_20200310_null_1":"test",
"epi_isl_422854_Netherlands_20200318_null_1":"test",
"epi_isl_422884_Noord_Brabant_20200101_null_6041":"test",
"epi_isl_422937_Zuid_Holland_20200324_null_1":"test",
"epi_isl_422956_Zuid_Holland_20200327_null_1":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}