{
"MLE":{
"content":{
"0":{
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"NAMES": [
["epi_isl_416620_unknown_20200217_null_1"],
["epi_isl_418861_Barcelona_20200324_null_1"],
["epi_isl_416636_Washington_20200312_null_1"],
["epi_isl_419875_Victoria_20200318_null_1"],
["epi_isl_419184_ARA_20200322_null_1"],
["epi_isl_417368_Connecticut_20200313_null_1"],
["epi_isl_418431_ARA_20200318_null_1"],
["epi_isl_418750_England_20200318_null_1"],
["epi_isl_418210_Touba_20200310_null_6"],
["epi_isl_418311_Derbyshire_20200325_null_1"],
["epi_isl_419898_Victoria_20200319_null_1"],
["epi_isl_420388_Vilvoorde_20200324_null_2"],
["epi_isl_420063_Ile_de_France_20200322_null_2"],
["epi_isl_417378_Connecticut_20200314_null_7"],
["epi_isl_415655_Wales_20200312_null_1"],
["epi_isl_420168_South_Yorkshire_20200325_null_1"],
["epi_isl_420485_England_20200318_null_2"],
["epi_isl_419546_Duesseldorf_20200315_null_1"],
["epi_isl_419595_Luxembourg_20200312_null_2"],
["Node27"],
["epi_isl_414010_England_20200226_null_1"],
["epi_isl_418305_South_Yorkshire_20200325_null_1"],
["Node24"],
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["epi_isl_418141_Wales_20200313_null_1"],
["epi_isl_417356_Connecticut_20200313_null_1"],
["epi_isl_417370_Idaho_20200314_null_20"],
["epi_isl_417952_Madrid_20200309_null_1"],
["epi_isl_420198_South_Yorkshire_20200328_null_1"],
["Node14"],
["epi_isl_420529_England_20200327_null_4026"]
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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":{
"Node14":{
"Global MG94xREV":0.005523989568333098,
"Nucleotide GTR":0.005475092697486506,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "I", "I"]
],
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["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAC", "ATT", "ATT"]
],
"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]
],
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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, 1, 0, 0]
]
},
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"Nucleotide GTR":0.005472308467871305,
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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, 0, 0, 0, 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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},
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"Nucleotide GTR":0.005473815726108259,
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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, 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]
],
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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]
]
},
"Node31":{
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["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "I", "I"]
],
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]
},
"epi_isl_414010_England_20200226_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
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],
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],
"original name":"epi_isl_414010_England_20200226_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_415655_Wales_20200312_null_1":{
"Global MG94xREV":0.005547324121935203,
"Nucleotide GTR":0.005498220699892297,
"amino-acid": [
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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, 1, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_415655_Wales_20200312_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_416620_unknown_20200217_null_1":{
"Global MG94xREV":0.005547324336534307,
"Nucleotide GTR":0.005498220912591832,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_416620_unknown_20200217_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416636_Washington_20200312_null_1":{
"Global MG94xREV":0.005553665136765373,
"Nucleotide GTR":0.005504505585763615,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416636_Washington_20200312_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417356_Connecticut_20200313_null_1":{
"Global MG94xREV":0.005524102482701011,
"Nucleotide GTR":0.005475204612366775,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417356_Connecticut_20200313_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417368_Connecticut_20200313_null_1":{
"Global MG94xREV":0.005547281624027588,
"Nucleotide GTR":0.005498178578164741,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417368_Connecticut_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_417370_Idaho_20200314_null_20":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417370_Idaho_20200314_null_20",
"synonymous substitution count": [
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]
},
"epi_isl_417378_Connecticut_20200314_null_7":{
"Global MG94xREV":0.005547238481961251,
"Nucleotide GTR":0.005498135817980378,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 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_417378_Connecticut_20200314_null_7",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_417952_Madrid_20200309_null_1":{
"Global MG94xREV":0.03538414728177215,
"Nucleotide GTR":0.03507093632106145,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "-", "T", "N", "M", "K", "I", "I"]
],
"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, 1, 2, 1, 2, 0, 0]
],
"original name":"epi_isl_417952_Madrid_20200309_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_418099_Wales_20200313_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "PL", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_418099_Wales_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418141_Wales_20200313_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"original name":"epi_isl_418141_Wales_20200313_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005547281360059701,
"Nucleotide GTR":0.00549817831653342,
"amino-acid": [
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],
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],
"original name":"epi_isl_418210_Touba_20200310_null_6",
"synonymous substitution count": [
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]
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"Nucleotide GTR":0,
"amino-acid": [
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],
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],
"original name":"epi_isl_418305_South_Yorkshire_20200325_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418311_Derbyshire_20200325_null_1":{
"Global MG94xREV":0.005543385155004264,
"Nucleotide GTR":0.005494316599637868,
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],
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],
"original name":"epi_isl_418311_Derbyshire_20200325_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418431_ARA_20200318_null_1":{
"Global MG94xREV":0.005547281522783881,
"Nucleotide GTR":0.005498178477817211,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418431_ARA_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418750_England_20200318_null_1":{
"Global MG94xREV":0.005543385157414726,
"Nucleotide GTR":0.005494316602026992,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_418750_England_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418861_Barcelona_20200324_null_1":{
"Global MG94xREV":0.005515983187317106,
"Nucleotide GTR":0.005467157186803202,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418861_Barcelona_20200324_null_1",
"synonymous substitution count": [
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]
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"epi_isl_419184_ARA_20200322_null_1":{
"Global MG94xREV":0.00552456904127813,
"Nucleotide GTR":0.005475667041092789,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_419184_ARA_20200322_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419546_Duesseldorf_20200315_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_419546_Duesseldorf_20200315_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419595_Luxembourg_20200312_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "T", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_419595_Luxembourg_20200312_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_419875_Victoria_20200318_null_1":{
"Global MG94xREV":0.005524610463663654,
"Nucleotide GTR":0.005475708096818487,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_419875_Victoria_20200318_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005547281522822496,
"Nucleotide GTR":0.005498178477855483,
"amino-acid": [
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"original name":"epi_isl_419898_Victoria_20200319_null_1",
"synonymous substitution count": [
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]
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"Nucleotide GTR":0.005494357391562548,
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],
"original name":"epi_isl_420063_Ile_de_France_20200322_null_2",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005524528906532911,
"Nucleotide GTR":0.005475627261609549,
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"original name":"epi_isl_420168_South_Yorkshire_20200325_null_1",
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"epi_isl_420198_South_Yorkshire_20200328_null_1":{
"Global MG94xREV":0.01119662935009344,
"Nucleotide GTR":0.01109751979666721,
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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, 2, 0, 0]
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"original name":"epi_isl_420198_South_Yorkshire_20200328_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_420388_Vilvoorde_20200324_null_2":{
"Global MG94xREV":0.005543426311217164,
"Nucleotide GTR":0.005494357391547028,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_420388_Vilvoorde_20200324_null_2",
"synonymous substitution count": [
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]
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"epi_isl_420485_England_20200318_null_2":{
"Global MG94xREV":0.005544269227734735,
"Nucleotide GTR":0.005495192846794158,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
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"original name":"epi_isl_420485_England_20200318_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_420529_England_20200327_null_4026":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_420529_England_20200327_null_4026",
"synonymous substitution count": [
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]
}
},
"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"amino-acid":{
"attribute type":"node label",
"display order":1
},
"codon":{
"attribute type":"node label",
"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
"attribute type":"branch label",
"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":918.4973460766964,
"Equilibrium frequencies": [
[0.05273360746367203],
[0.01860820714282872],
[0.03169283447496222],
[0.06504519478017715],
[0.01814138521211908],
[0.006401584684255067],
[0.01090295062916565],
[0.02237681037690082],
[0.004366189181879926],
[0.001540705379907305],
[0.002624074431528669],
[0.005385552770652535],
[0.05409635974135546],
[0.0190890840994254],
[0.03251184695000959],
[0.06672610552386396],
[0.02088226607747449],
[0.007368764464843465],
[0.01255021672301561],
[0.0257575980440279],
[0.007183905126809469],
[0.002534998099384555],
[0.004317518315519218],
[0.008861114016854268],
[0.001728990839540382],
[0.0006101122460166392],
[0.001039121408942645],
[0.002132654133486338],
[0.02142190971326925],
[0.007559189528501321],
[0.01287454189717503],
[0.02642323096941299],
[0.0266744860804173],
[0.009412676019838957],
[0.01603133395783201],
[0.03290211358965218],
[0.009176541310084345],
[0.003238143373187763],
[0.005515090258020146],
[0.01131896613244169],
[0.00220856979368911],
[0.0007793421726111448],
[0.001327347781886727],
[0.002724199221816721],
[0.02736381340715414],
[0.009655920248748732],
[0.01644561884968944],
[0.033752376493926],
[0.01242569887845754],
[0.04343416846262795],
[0.01211397681429868],
[0.004274681758481719],
[0.007280485452727343],
[0.01494219757279885],
[0.001028811693904944],
[0.001752235369617575],
[0.003596222704773609],
[0.03612304352629934],
[0.01274680623793587],
[0.02170990558534303],
[0.04455660280475992]
],
"Log Likelihood":-411.9895000622271,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[1.255839486150189, 1]
]
},
"display order":1,
"estimated parameters":46
},
"Nucleotide GTR":{
"AIC-c":974.015161667929,
"Equilibrium frequencies": [
[0.3607372732592159],
[0.1430661205383265],
[0.139945387165984],
[0.3562512190364736]
],
"Log Likelihood":-425.2844450787064,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.3104135338887669,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.2574151195882901,
"Substitution rate from nucleotide C to nucleotide G":1.618325897678095,
"Substitution rate from nucleotide C to nucleotide T":3.948684938945854,
"Substitution rate from nucleotide G to nucleotide T":3.010477611095681
},
"display order":0,
"estimated parameters":61
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-06/sequences.ORF6.compressed.fas",
"number of sequences":28,
"number of sites":63,
"partition count":1,
"trees":{
"0":"(epi_isl_416620_unknown_20200217_null_1,epi_isl_418861_Barcelona_20200324_null_1,epi_isl_416636_Washington_20200312_null_1,epi_isl_419875_Victoria_20200318_null_1,epi_isl_419184_ARA_20200322_null_1,epi_isl_417368_Connecticut_20200313_null_1,epi_isl_418431_ARA_20200318_null_1,epi_isl_418750_England_20200318_null_1,epi_isl_418210_Touba_20200310_null_6,epi_isl_418311_Derbyshire_20200325_null_1,epi_isl_419898_Victoria_20200319_null_1,epi_isl_420388_Vilvoorde_20200324_null_2,epi_isl_420063_Ile_de_France_20200322_null_2,epi_isl_417378_Connecticut_20200314_null_7,epi_isl_415655_Wales_20200312_null_1,epi_isl_420168_South_Yorkshire_20200325_null_1,epi_isl_420485_England_20200318_null_2,(epi_isl_419546_Duesseldorf_20200315_null_1,epi_isl_419595_Luxembourg_20200312_null_2)Node27,(epi_isl_414010_England_20200226_null_1,epi_isl_418305_South_Yorkshire_20200325_null_1)Node24,epi_isl_418099_Wales_20200313_null_1,epi_isl_418141_Wales_20200313_null_1,(epi_isl_417356_Connecticut_20200313_null_1,epi_isl_417370_Idaho_20200314_null_20,epi_isl_417952_Madrid_20200309_null_1,epi_isl_420198_South_Yorkshire_20200328_null_1)Node14,epi_isl_420529_England_20200327_null_4026)"
}
},
"tested":{
"0":{
"Node14":"test",
"Node24":"test",
"Node27":"test",
"epi_isl_414010_England_20200226_null_1":"test",
"epi_isl_415655_Wales_20200312_null_1":"test",
"epi_isl_416620_unknown_20200217_null_1":"test",
"epi_isl_416636_Washington_20200312_null_1":"test",
"epi_isl_417356_Connecticut_20200313_null_1":"test",
"epi_isl_417368_Connecticut_20200313_null_1":"test",
"epi_isl_417370_Idaho_20200314_null_20":"test",
"epi_isl_417378_Connecticut_20200314_null_7":"test",
"epi_isl_417952_Madrid_20200309_null_1":"test",
"epi_isl_418099_Wales_20200313_null_1":"test",
"epi_isl_418141_Wales_20200313_null_1":"test",
"epi_isl_418210_Touba_20200310_null_6":"test",
"epi_isl_418305_South_Yorkshire_20200325_null_1":"test",
"epi_isl_418311_Derbyshire_20200325_null_1":"test",
"epi_isl_418431_ARA_20200318_null_1":"test",
"epi_isl_418750_England_20200318_null_1":"test",
"epi_isl_418861_Barcelona_20200324_null_1":"test",
"epi_isl_419184_ARA_20200322_null_1":"test",
"epi_isl_419546_Duesseldorf_20200315_null_1":"test",
"epi_isl_419595_Luxembourg_20200312_null_2":"test",
"epi_isl_419875_Victoria_20200318_null_1":"test",
"epi_isl_419898_Victoria_20200319_null_1":"test",
"epi_isl_420063_Ile_de_France_20200322_null_2":"test",
"epi_isl_420168_South_Yorkshire_20200325_null_1":"test",
"epi_isl_420198_South_Yorkshire_20200328_null_1":"test",
"epi_isl_420388_Vilvoorde_20200324_null_2":"test",
"epi_isl_420485_England_20200318_null_2":"test",
"epi_isl_420529_England_20200327_null_4026":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}