{
"MLE":{
"content":{
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"NAMES": [
["epi_isl_420168_South_Yorkshire_20200325_null_1"],
["epi_isl_421901_England_20200326_null_4"],
["epi_isl_422884_Noord_Brabant_20200101_null_1"],
["epi_isl_420388_Vilvoorde_20200324_null_2"],
["epi_isl_419898_Victoria_20200319_null_1"],
["epi_isl_421909_England_20200326_null_2"],
["epi_isl_418431_ARA_20200318_null_1"],
["epi_isl_418861_Barcelona_20200324_null_1"],
["epi_isl_416636_Washington_20200312_null_1"],
["epi_isl_421930_England_20200330_null_1"],
["Node67"],
["epi_isl_420063_Ile_de_France_20200322_null_2"],
["epi_isl_416620_unknown_20200217_null_1"],
["epi_isl_419875_Victoria_20200318_null_1"],
["epi_isl_422093_Wales_20200329_null_1"],
["epi_isl_417368_USA_20200313_null_1"],
["epi_isl_422183_Wales_20200324_null_2"],
["epi_isl_418210_Touba_20200310_null_6"],
["epi_isl_421323_Wisconsin_20200322_null_2"],
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["epi_isl_423042_Bangkok_20200324_null_6092"],
["epi_isl_415655_Wales_20200312_null_1"],
["epi_isl_421845_England_20200324_null_1"],
["epi_isl_422619_Netherlands_20200402_null_2"],
["epi_isl_417356_Washington_20200313_null_2"],
["epi_isl_422999_Washington_20200318_null_28"],
["Node26"],
["epi_isl_417952_Madrid_20200309_null_1"],
["epi_isl_422464_Wisconsin_20200326_null_1"],
["epi_isl_419184_ARA_20200322_null_1"],
["epi_isl_417378_Washington_20200314_null_8"],
["epi_isl_422623_Netherlands_20200402_null_3"]
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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":{
"Node26":{
"Global MG94xREV":0.005590260257943487,
"Nucleotide GTR":0.005475728127715971,
"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": [
["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", "---", "---"]
],
"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]
],
"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, 1, 0, 0]
]
},
"Node37":{
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"Nucleotide GTR":0.004073160292280095,
"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": [
["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTC", "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", "GAT", "---", "---"]
],
"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]
],
"synonymous substitution count": [
[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, 0, 0, 0, 0]
]
},
"Node40":{
"Global MG94xREV":0.00428786830023836,
"Nucleotide GTR":0.004200019315056759,
"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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"Node67":{
"Global MG94xREV":0.005572666064403428,
"Nucleotide GTR":0.005458494400482094,
"amino-acid": [
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],
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],
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]
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"Nucleotide GTR":0,
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],
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],
"original name":"epi_isl_414010_England_20200226_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005614339277395228,
"Nucleotide GTR":0.005499313821049719,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_415655_Wales_20200312_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005613534142494561,
"Nucleotide GTR":0.005498525181591315,
"amino-acid": [
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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":0.005565065266420137,
"Nucleotide GTR":0.005451049326122443,
"amino-acid": [
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"codon": [
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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_Washington_20200313_null_2":{
"Global MG94xREV":0.005591265455257108,
"Nucleotide GTR":0.005476712730748769,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417356_Washington_20200313_null_2",
"synonymous substitution count": [
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]
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"epi_isl_417368_USA_20200313_null_1":{
"Global MG94xREV":0.005613660778669633,
"Nucleotide GTR":0.005498649223269845,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417368_USA_20200313_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417378_Washington_20200314_null_8":{
"Global MG94xREV":0.005613597477751254,
"Nucleotide GTR":0.005498587219247983,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417378_Washington_20200314_null_8",
"synonymous substitution count": [
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]
},
"epi_isl_417952_Madrid_20200309_null_1":{
"Global MG94xREV":0.03607193312948224,
"Nucleotide GTR":0.03533289860298174,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"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", "HPRL", "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_418099_Wales_20200313_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_418141_Wales_20200313_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "TPAS", "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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"codon": [
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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_418141_Wales_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418210_Touba_20200310_null_6":{
"Global MG94xREV":0.005613882455944787,
"Nucleotide GTR":0.005498866358865476,
"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, 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_418210_Touba_20200310_null_6",
"synonymous substitution count": [
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]
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"epi_isl_418305_South_Yorkshire_20200325_null_1":{
"Global MG94xREV":0.001425300491508051,
"Nucleotide GTR":0.001396099221088703,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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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_418431_ARA_20200318_null_1":{
"Global MG94xREV":0.005613787453887601,
"Nucleotide GTR":0.005498773303191373,
"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_418861_Barcelona_20200324_null_1":{
"Global MG94xREV":0.00557376171519514,
"Nucleotide GTR":0.005459567603800286,
"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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]
},
"epi_isl_419184_ARA_20200322_null_1":{
"Global MG94xREV":0.005587221442277066,
"Nucleotide GTR":0.00547275157069505,
"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": [
[0, 0, 0, 0, 0, 0, 0, 0, 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]
],
"original name":"epi_isl_419546_Duesseldorf_20200315_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419875_Victoria_20200318_null_1":{
"Global MG94xREV":0.005588562851585688,
"Nucleotide GTR":0.00547406549747897,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "T", "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": [
[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_419875_Victoria_20200318_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419898_Victoria_20200319_null_1":{
"Global MG94xREV":0.005613724116356018,
"Nucleotide GTR":0.005498711263306429,
"amino-acid": [
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],
"codon": [
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],
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[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, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_419898_Victoria_20200319_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_420063_Ile_de_France_20200322_null_2":{
"Global MG94xREV":0.005605744010681727,
"Nucleotide GTR":0.005490894652435623,
"amino-acid": [
["M", "F", "Y", "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": [
[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, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_420063_Ile_de_France_20200322_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, 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_420168_South_Yorkshire_20200325_null_1":{
"Global MG94xREV":0.005587191665274888,
"Nucleotide GTR":0.005472722403758113,
"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, 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_420168_South_Yorkshire_20200325_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_420388_Vilvoorde_20200324_null_2":{
"Global MG94xREV":0.005605863146339619,
"Nucleotide GTR":0.005491011347266061,
"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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]
},
"epi_isl_421323_Wisconsin_20200322_null_2":{
"Global MG94xREV":0.005573674309075266,
"Nucleotide GTR":0.005459481988439444,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421323_Wisconsin_20200322_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_421808_England_20200325_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_421808_England_20200325_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_421845_England_20200324_null_1":{
"Global MG94xREV":0.005611746205698841,
"Nucleotide GTR":0.005496773875685837,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421845_England_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_421901_England_20200326_null_4":{
"Global MG94xREV":0.005613502472625834,
"Nucleotide GTR":0.005498494160568501,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421901_England_20200326_null_4",
"synonymous substitution count": [
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]
},
"epi_isl_421909_England_20200326_null_2":{
"Global MG94xREV":0.005606585176473267,
"Nucleotide GTR":0.005491718584591247,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421909_England_20200326_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_421930_England_20200330_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_421930_England_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422093_Wales_20200329_null_1":{
"Global MG94xREV":0.0056058333572929,
"Nucleotide GTR":0.005490982168531352,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422093_Wales_20200329_null_1",
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"Global MG94xREV":0.005606647467839266,
"Nucleotide GTR":0.005491779599744234,
"amino-acid": [
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"original name":"epi_isl_422183_Wales_20200324_null_2",
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"Nucleotide GTR":0.001270684164096036,
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"original name":"epi_isl_422278_Wales_20200328_null_3",
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"Nucleotide GTR":0.01817422675480032,
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"Nucleotide GTR":0.01117470871655039,
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"original name":"epi_isl_422619_Netherlands_20200402_null_2",
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"epi_isl_422623_Netherlands_20200402_null_3":{
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"Nucleotide GTR":0.005491840550240891,
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],
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"original name":"epi_isl_422623_Netherlands_20200402_null_3",
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]
},
"epi_isl_422884_Noord_Brabant_20200101_null_1":{
"Global MG94xREV":0.005606803077051616,
"Nucleotide GTR":0.005491932020866283,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_422884_Noord_Brabant_20200101_null_1",
"synonymous substitution count": [
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]
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"epi_isl_422999_Washington_20200318_null_28":{
"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_422999_Washington_20200318_null_28",
"synonymous substitution count": [
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]
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"epi_isl_423042_Bangkok_20200324_null_6092":{
"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_423042_Bangkok_20200324_null_6092",
"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":{
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"nonsynonymous substitution count":{
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"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
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"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":{
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"Equilibrium frequencies": [
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[0.01851688092755363],
[0.03164563442317073],
[0.06494892975516092],
[0.01797286494735569],
[0.006330481511137453],
[0.01081889030922035],
[0.02220449548667761],
[0.004458253837356882],
[0.001570305767723343],
[0.002683676719226742],
[0.005507929731849383],
[0.0540474156361789],
[0.01903681835988709],
[0.03253421549527033],
[0.06677263753304344],
[0.02075982404751521],
[0.007312116498521691],
[0.01249651960701049],
[0.02564763162230811],
[0.007097290457363451],
[0.002499838848793106],
[0.004272263057436968],
[0.008768315702019056],
[0.001760516339996888],
[0.0006200968055482663],
[0.001059754982069163],
[0.002175022025714075],
[0.02134274131382963],
[0.007517434180913177],
[0.01284741068542669],
[0.02636779414769833],
[0.02668733899008982],
[0.009399931872468533],
[0.01606462820615814],
[0.03297075340479146],
[0.009123766941052597],
[0.003213613305471278],
[0.005492114586698757],
[0.01127191699584363],
[0.002263193380423314],
[0.0007971519227938324],
[0.001362344901776826],
[0.002796052123480833],
[0.02743669556718332],
[0.009663873540668605],
[0.01651570857836448],
[0.03389654263109024],
[0.01243529989447511],
[0.0436174657325146],
[0.0120699574867761],
[0.004251333492687987],
[0.007265594353981727],
[0.01491177490759156],
[0.001054563304914203],
[0.001802264914591887],
[0.003698936029303067],
[0.03629638407174344],
[0.01278447197819299],
[0.02184885932452857],
[0.04484220510555391]
],
"Log Likelihood":-466.4029866828255,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.8748107257441432, 1]
]
},
"display order":1,
"estimated parameters":55
},
"Nucleotide GTR":{
"AIC-c":1113.801203766933,
"Equilibrium frequencies": [
[0.3602874087591241],
[0.1423737834549878],
[0.140396897810219],
[0.3569419099756691]
],
"Log Likelihood":-479.0076491626813,
"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":0.1053567926079529,
"Substitution rate from nucleotide C to nucleotide G":0.6882669386156605,
"Substitution rate from nucleotide C to nucleotide T":2.260956773917624,
"Substitution rate from nucleotide G to nucleotide T":1.581763739903502
},
"display order":0,
"estimated parameters":77
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-12/sequences.ORF6.compressed.fas",
"number of sequences":36,
"number of sites":63,
"partition count":1,
"trees":{
"0":"(epi_isl_420168_South_Yorkshire_20200325_null_1,epi_isl_421901_England_20200326_null_4,epi_isl_422884_Noord_Brabant_20200101_null_1,epi_isl_420388_Vilvoorde_20200324_null_2,epi_isl_419898_Victoria_20200319_null_1,epi_isl_421909_England_20200326_null_2,epi_isl_418431_ARA_20200318_null_1,epi_isl_418861_Barcelona_20200324_null_1,(epi_isl_416636_Washington_20200312_null_1,epi_isl_421930_England_20200330_null_1)Node67,epi_isl_420063_Ile_de_France_20200322_null_2,epi_isl_416620_unknown_20200217_null_1,epi_isl_419875_Victoria_20200318_null_1,epi_isl_422093_Wales_20200329_null_1,epi_isl_417368_USA_20200313_null_1,epi_isl_422183_Wales_20200324_null_2,epi_isl_418210_Touba_20200310_null_6,epi_isl_421323_Wisconsin_20200322_null_2,(epi_isl_419546_Duesseldorf_20200315_null_1,epi_isl_422278_Wales_20200328_null_3)Node40,(epi_isl_414010_England_20200226_null_1,epi_isl_418305_South_Yorkshire_20200325_null_1)Node37,epi_isl_418099_Wales_20200313_null_1,epi_isl_418141_Wales_20200313_null_1,epi_isl_421808_England_20200325_null_1,epi_isl_423042_Bangkok_20200324_null_6092,epi_isl_415655_Wales_20200312_null_1,epi_isl_421845_England_20200324_null_1,(epi_isl_422619_Netherlands_20200402_null_2,epi_isl_417356_Washington_20200313_null_2,epi_isl_422999_Washington_20200318_null_28)Node26,epi_isl_417952_Madrid_20200309_null_1,epi_isl_422464_Wisconsin_20200326_null_1,epi_isl_419184_ARA_20200322_null_1,epi_isl_417378_Washington_20200314_null_8,epi_isl_422623_Netherlands_20200402_null_3)"
}
},
"tested":{
"0":{
"Node26":"test",
"Node37":"test",
"Node40":"test",
"Node67":"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_Washington_20200313_null_2":"test",
"epi_isl_417368_USA_20200313_null_1":"test",
"epi_isl_417378_Washington_20200314_null_8":"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_418431_ARA_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_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_420388_Vilvoorde_20200324_null_2":"test",
"epi_isl_421323_Wisconsin_20200322_null_2":"test",
"epi_isl_421808_England_20200325_null_1":"test",
"epi_isl_421845_England_20200324_null_1":"test",
"epi_isl_421901_England_20200326_null_4":"test",
"epi_isl_421909_England_20200326_null_2":"test",
"epi_isl_421930_England_20200330_null_1":"test",
"epi_isl_422093_Wales_20200329_null_1":"test",
"epi_isl_422183_Wales_20200324_null_2":"test",
"epi_isl_422278_Wales_20200328_null_3":"test",
"epi_isl_422464_Wisconsin_20200326_null_1":"test",
"epi_isl_422619_Netherlands_20200402_null_2":"test",
"epi_isl_422623_Netherlands_20200402_null_3":"test",
"epi_isl_422884_Noord_Brabant_20200101_null_1":"test",
"epi_isl_422999_Washington_20200318_null_28":"test",
"epi_isl_423042_Bangkok_20200324_null_6092":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":0
},
"Total time":{
"order":0,
"timer":1
}
}
}