{
"MLE":{
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[0.151523872743264, 0.7059589890561473, 0, 0, 0.1767077564970734, 0, 0, 0, 1, 1, 3.133823777687699],
[0, 1.072074017013903, 0, 0, 0, null, 0, null, 1, 1, 3.215685937108336],
[0.3063063675721901, 1.111771640224361, 1, 1, 0.216001070384088, 3.264705229362627, 0.8994652892910592, -0.7355320097579177, 0.9533435375929282, 0.3853456783611042, 3.215685937108336],
[0.2858276205998038, 0.480280718212315, 1, 0, 0.3730903399941982, 3.498612198154675, 0, -1.116403616267197, 1, 0.3730903399941982, 3.133823777687699],
[0.2870607847958664, 0.5741215695917329, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 3.12036140496353],
[0.09488696913985206, 0.6630747466518966, 0, 0, 0.1251870208784034, 0, 0, 0, 1, 1, 3.12036140496353],
[0.4821294395788919, 0.3790529148087073, 0, 0, 0.5598459340492897, 0, 0, 0, 1, 1, 3.12036140496353],
[0.09488696913985206, 0.5712267304647216, 0, 0, 0.1424486077920031, 0, 0, 0, 1, 1, 3.12036140496353],
[0.1521776017787002, 0.7090047526088991, 0, 0, 0.1767077564970734, 0, 0, 0, 1, 1, 3.12036140496353],
[0.1521776017787002, 0.7090047526088991, 0, 0, 0.1767077564970734, 0, 0, 0, 1, 1, 3.12036140496353],
[0.1521776017787002, 0.7090047526088991, 0, 0, 0.1767077564970734, 0, 0, 0, 1, 1, 3.12036140496353],
[0.09488696913985206, 0.6630747466518966, 0, 0, 0.1251870208784034, 0, 0, 0, 1, 1, 3.12036140496353],
[0.2692377297110612, 0.5919446246765381, 1, 1, 0.31263730421244, 3.71418969055033, 1.689347209709759, -0.6489128078624716, 0.9022579160147784, 0.5275325244396581, 3.12036140496353],
[0.1521776017787002, 0.6241364719398315, 0, 0, 0.196025818583672, 0, 0, 0, 1, 1, 3.12036140496353],
[0.2544771258872309, 0.6063658009371917, 1, 2, 0.2956138895465816, 3.929626273927427, 3.298339050303998, -0.2023122137773036, 0.7895032448537376, 0.6505119335273259, 3.12036140496353],
[0.2870607847958664, 0.5741215695917329, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 3.12036140496353],
[0.09488696913985206, 0.6440752984066368, 0, 0, 0.1284057025738227, 0, 0, 0, 1, 1, 3.12036140496353]
]
}
}
},
"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":{
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "I", "C", "S", "A", "K"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ATC", "TGT", "TCT", "GCC", "AAA"]
],
"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]
],
"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]
]
},
"Node15":{
"Global MG94xREV":0.5249913239844114,
"Nucleotide GTR":0.4354824066363353,
"amino-acid": [
["M", "N", "D", "L", "C", "P", "I", "H", "F", "Y", "S", "K", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "W", "Y", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["ATG", "AAT", "GAT", "CTT", "TGT", "CCA", "ATT", "CAC", "TTC", "TAT", "TCT", "AAA", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TGG", "TAT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 1, 1, 0, 1, 1.5, 0, 1, 0, 0, 1.5, 3, 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]
],
"synonymous substitution count": [
[0, 0, 0, 0, 1, 0.5, 0, 0, 0, 0, 0.5, 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]
]
},
"Node16":{
"Global MG94xREV":0.3406905006346166,
"Nucleotide GTR":0.2826041352616837,
"amino-acid": [
["V", "D", "D", "L", "C", "P", "I", "H", "F", "Y", "S", "K", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "W", "Y", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[1.5, 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]
],
"synonymous substitution count": [
[0.5, 0, 1, 1, 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]
]
},
"Node17":{
"Global MG94xREV":0.03291191035876472,
"Nucleotide GTR":0.0273005615050122,
"amino-acid": [
["V", "D", "D", "P", "C", "P", "I", "H", "F", "Y", "S", "K", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"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]
]
},
"Node2":{
"Global MG94xREV":0.01966096271576069,
"Nucleotide GTR":0.0163088473448772,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "S", "A", "K"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "TCT", "GCC", "AAA"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]
],
"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, 1, 0, 0, 0, 0]
]
},
"Node3":{
"Global MG94xREV":0.01355852681012064,
"Nucleotide GTR":0.01124685231158208,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "S", "A", "K"]
],
"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]
],
"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]
]
},
"Node4":{
"Global MG94xREV":0.01608125268657222,
"Nucleotide GTR":0.0133394635334649,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "K"]
],
"codon": [
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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 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, 1, 0, 0]
]
},
"Node5":{
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"Nucleotide GTR":0.2554697769608607,
"amino-acid": [
["-", "-", "-", "-", "-", "F", "I", "D", "F", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
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],
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]
},
"Node7":{
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"Nucleotide GTR":0.552616222491097,
"amino-acid": [
["-", "-", "-", "-", "-", "F", "M", "T", "L", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
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]
},
"epi_isl_413747_China_20200201_null_1":{
"Global MG94xREV":0.6051312378993068,
"Nucleotide GTR":0.5019587863113711,
"amino-acid": [
["-", "-", "-", "-", "-", "V", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
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],
"original name":"epi_isl_413747_China_20200201_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424220_Washington_20200321_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
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],
"original name":"epi_isl_424220_Washington_20200321_null_1",
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]
},
"epi_isl_428830_Singapore_20200227_null_16":{
"Global MG94xREV":0.01346237272416856,
"Nucleotide GTR":0.01116709211204102,
"amino-acid": [
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],
"codon": [
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],
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"original name":"epi_isl_428830_Singapore_20200227_null_16",
"synonymous substitution count": [
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},
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"Log Likelihood":-306.5727043786451,
"Rate Distributions":{
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"estimated parameters":38
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"Substitution rate from nucleotide C to nucleotide T":0.7715346422641334,
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},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-06-25/sequences.ORF7b.compressed.fas",
"number of sequences":15,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_474778_Wales_20200501_null_11,((((epi_isl_449375_England_20200328_null_5,(epi_isl_430896_Washington_20200329_null_1,epi_isl_472891_Wales_20200519_null_3)Node7,epi_isl_413747_China_20200201_null_1)Node5,epi_isl_463896_Zhejiang_20200131_null_1)Node4,epi_isl_428830_Singapore_20200227_null_16)Node3,epi_isl_458628_England_20200326_null_2)Node2,(((epi_isl_450857_Florida_20200410_null_1,epi_isl_453320_England_20200410_null_1,epi_isl_449506_England_20200331_null_2,epi_isl_453338_England_20200411_null_6)Node17,epi_isl_449433_England_20200327_null_2)Node16,epi_isl_424220_Washington_20200321_null_1,epi_isl_460625_Washington_20200331_null_2)Node15)"
}
},
"tested":{
"0":{
"Node15":"test",
"Node16":"test",
"Node17":"test",
"Node2":"test",
"Node3":"test",
"Node4":"test",
"Node5":"test",
"Node7":"test",
"epi_isl_413747_China_20200201_null_1":"test",
"epi_isl_424220_Washington_20200321_null_1":"test",
"epi_isl_428830_Singapore_20200227_null_16":"test",
"epi_isl_430896_Washington_20200329_null_1":"test",
"epi_isl_449375_England_20200328_null_5":"test",
"epi_isl_449433_England_20200327_null_2":"test",
"epi_isl_449506_England_20200331_null_2":"test",
"epi_isl_450857_Florida_20200410_null_1":"test",
"epi_isl_453320_England_20200410_null_1":"test",
"epi_isl_453338_England_20200411_null_6":"test",
"epi_isl_458628_England_20200326_null_2":"test",
"epi_isl_460625_Washington_20200331_null_2":"test",
"epi_isl_463896_Zhejiang_20200131_null_1":"test",
"epi_isl_472891_Wales_20200519_null_3":"test",
"epi_isl_474778_Wales_20200501_null_11":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}