{
"MLE":{
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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":{
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"Nucleotide GTR":0.001857862342447042,
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],
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],
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],
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],
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],
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],
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"Nucleotide GTR":1.479901062362232,
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],
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],
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],
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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, 18.5, 0, 0, 0, 0, 0, 0, 0, 0, 0]
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"synonymous substitution count": [
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]
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"epi_isl_413875_Guangdong_20200210_null_1":{
"Global MG94xREV":0.003218175551570014,
"Nucleotide GTR":0.003031124048034786,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "ILVF", "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", "V", "-"]
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"codon": [
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[0, 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]
],
"original name":"epi_isl_413875_Guangdong_20200210_null_1",
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]
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"epi_isl_414509_North_Rhine_Westphalia_20200228_null_1":{
"Global MG94xREV":0.008287595512495407,
"Nucleotide GTR":0.007805891771831597,
"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", "F", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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],
"original name":"epi_isl_414509_North_Rhine_Westphalia_20200228_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416633_unknown_20200217_null_1":{
"Global MG94xREV":0.008286749064379708,
"Nucleotide GTR":0.007805094522210563,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_416633_unknown_20200217_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417253_England_20200303_null_1":{
"Global MG94xREV":0.008248127146573438,
"Nucleotide GTR":0.007768717443966141,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417253_England_20200303_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417453_Idaho_20200314_null_1":{
"Global MG94xREV":0.008299528659083224,
"Nucleotide GTR":0.007817131322630313,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417453_Idaho_20200314_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417576_Reykjavik_20200317_null_2":{
"Global MG94xREV":0.008303021649826188,
"Nucleotide GTR":0.007820421288659484,
"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", "-"]
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417576_Reykjavik_20200317_null_2",
"synonymous substitution count": [
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]
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"epi_isl_418004_Portugal_20200312_null_1":{
"Global MG94xREV":0.008316307490133965,
"Nucleotide GTR":0.007832934909936484,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "S", "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", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418004_Portugal_20200312_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418035_Washington_20200314_null_1":{
"Global MG94xREV":2715.463171198225,
"Nucleotide GTR":2557.631051468345,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "KNTRSIM", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418035_Washington_20200314_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418052_Idaho_20200316_null_1":{
"Global MG94xREV":0.3723296549480921,
"Nucleotide GTR":0.3506885664950969,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "P", "Q", "EDAGV", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418052_Idaho_20200316_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418065_Idaho_20200313_null_1":{
"Global MG94xREV":1.713718933146649,
"Nucleotide GTR":1.614111656307608,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "P", "I", "I", "L", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418065_Idaho_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418078_Washington_20200315_null_1":{
"Global MG94xREV":0.3590188655777977,
"Nucleotide GTR":0.3381514462814585,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "KNTRSIM", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418078_Washington_20200315_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418638_Li_ge_20200319_null_1":{
"Global MG94xREV":0.008247147820891591,
"Nucleotide GTR":0.007767795040083084,
"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", "S", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418638_Li_ge_20200319_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418954_Washington_20200323_null_1":{
"Global MG94xREV":0.008244285964265958,
"Nucleotide GTR":0.007765099524471525,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_418954_Washington_20200323_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418991_Hangzhou_20200204_null_1":{
"Global MG94xREV":8.297325845344795e-05,
"Nucleotide GTR":7.815056544051925e-05,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "T", "N", "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", "-"]
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"codon": [
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],
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"original name":"epi_isl_418991_Hangzhou_20200204_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419431_Wales_20200317_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
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],
"original name":"epi_isl_419431_Wales_20200317_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419497_Wales_20200320_null_1":{
"Global MG94xREV":0.006484801601032404,
"Nucleotide GTR":0.006107882483301557,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_419497_Wales_20200320_null_1",
"synonymous substitution count": [
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]
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"epi_isl_419575_Luxembourg_20200314_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
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"codon": [
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],
"nonsynonymous substitution count": [
[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]
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"original name":"epi_isl_419575_Luxembourg_20200314_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_420084_Taiwan_20200321_null_1":{
"Global MG94xREV":0.008301711427132976,
"Nucleotide GTR":0.007819187220644855,
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"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, 1, 0, 0, 0]
],
"original name":"epi_isl_420084_Taiwan_20200321_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]
]
},
"epi_isl_420106_Singapore_20200306_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_420106_Singapore_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_420107_Singapore_20200309_null_14":{
"Global MG94xREV":0.009107435144742668,
"Nucleotide GTR":0.008578079486583309,
"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]
],
"original name":"epi_isl_420107_Singapore_20200309_null_14",
"synonymous substitution count": [
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]
},
"epi_isl_420388_Vilvoorde_20200324_null_1":{
"Global MG94xREV":0.008301046326611728,
"Nucleotide GTR":0.007818560778068291,
"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", "K", "T", "C", "H", "A", "-"]
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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, 1, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_420388_Vilvoorde_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_421520_Comunitat_Valenciana_20200320_null_4456":{
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_421520_Comunitat_Valenciana_20200320_null_4456",
"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]
]
}
},
"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]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":686.1016415668748,
"Equilibrium frequencies": [
[0.01438172294195769],
[0.01133294277203782],
[0.00835711635161931],
[0.02187915996506703],
[0.006398719907410867],
[0.005042255842199902],
[0.003718250378168959],
[0.009734481535412207],
[0.004067288562317717],
[0.00320506442101131],
[0.002363472296614321],
[0.006187635336752176],
[0.03137766246126149],
[0.02472591458123239],
[0.01823333526093534],
[0.04773537211713023],
[0.0152249112270135],
[0.01199738364738745],
[0.008847087034059295],
[0.02316191665867466],
[0.006773871458240828],
[0.005337879049068498],
[0.003936248261484436],
[0.01030520597676585],
[0.004305750259954966],
[0.003392974644532697],
[0.00250204068376807],
[0.006550411177254956],
[0.03321730834420254],
[0.0261755740967388],
[0.01930234032740501],
[0.05053405671941232],
[0.01184096431823287],
[0.009330799343434448],
[0.006880699685442171],
[0.01801386061356027],
[0.005268284920506523],
[0.004151461667830114],
[0.003061362691510821],
[0.008014731543814759],
[0.003348737764781678],
[0.002638839143265166],
[0.001945927566835226],
[0.005094491774901757],
[0.02583430254447502],
[0.0203576910411676],
[0.01501212845626712],
[0.03930216429823435],
[0.02182327990983313],
[0.04213160180141066],
[0.01232169423360985],
[0.009709619366721057],
[0.007160048401359146],
[0.01874520321840498],
[0.006171831923598428],
[0.004551220148698934],
[0.01191521925506346],
[0.06042239201083013],
[0.04761345449164667],
[0.03511101989070332],
[0.09192161367676764]
],
"Log Likelihood":-296.0013158329424,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.4478149915019596, 1]
]
},
"display order":1,
"estimated parameters":45
},
"Nucleotide GTR":{
"AIC-c":717.5966946474518,
"Equilibrium frequencies": [
[0.2262977262977263],
[0.1881166881166881],
[0.1297726297726298],
[0.4558129558129558]
],
"Log Likelihood":-304.8792721792173,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.1381076022657589,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.0641202385772785,
"Substitution rate from nucleotide C to nucleotide G":0.1160260307985232,
"Substitution rate from nucleotide C to nucleotide T":0.6838877978714094,
"Substitution rate from nucleotide G to nucleotide T":0.4149967919321761
},
"display order":0,
"estimated parameters":53
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-08/sequences.ORF7b.compressed.fas",
"number of sequences":24,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_420106_Singapore_20200306_null_1,epi_isl_419575_Luxembourg_20200314_null_1,epi_isl_414509_North_Rhine_Westphalia_20200228_null_1,epi_isl_419431_Wales_20200317_null_1,epi_isl_416633_unknown_20200217_null_1,(epi_isl_419497_Wales_20200320_null_1,((epi_isl_413752_China_20200201_null_1,epi_isl_418035_Washington_20200314_null_1)Node25,epi_isl_413747_China_20200201_null_1)Node24,epi_isl_418065_Idaho_20200313_null_1)Node22,epi_isl_417253_England_20200303_null_1,epi_isl_421520_Comunitat_Valenciana_20200320_null_4456,epi_isl_418638_Li_ge_20200319_null_1,(epi_isl_418991_Hangzhou_20200204_null_1,epi_isl_418052_Idaho_20200316_null_1)Node36,epi_isl_418004_Portugal_20200312_null_1,epi_isl_418954_Washington_20200323_null_1,epi_isl_417576_Reykjavik_20200317_null_2,epi_isl_417453_Idaho_20200314_null_1,epi_isl_420388_Vilvoorde_20200324_null_1,((epi_isl_418078_Washington_20200315_null_1,epi_isl_420107_Singapore_20200309_null_14)Node8,epi_isl_413875_Guangdong_20200210_null_1)Node7,epi_isl_420084_Taiwan_20200321_null_1)"
}
},
"tested":{
"0":{
"Node22":"test",
"Node24":"test",
"Node25":"test",
"Node36":"test",
"Node7":"test",
"Node8":"test",
"epi_isl_413747_China_20200201_null_1":"test",
"epi_isl_413752_China_20200201_null_1":"test",
"epi_isl_413875_Guangdong_20200210_null_1":"test",
"epi_isl_414509_North_Rhine_Westphalia_20200228_null_1":"test",
"epi_isl_416633_unknown_20200217_null_1":"test",
"epi_isl_417253_England_20200303_null_1":"test",
"epi_isl_417453_Idaho_20200314_null_1":"test",
"epi_isl_417576_Reykjavik_20200317_null_2":"test",
"epi_isl_418004_Portugal_20200312_null_1":"test",
"epi_isl_418035_Washington_20200314_null_1":"test",
"epi_isl_418052_Idaho_20200316_null_1":"test",
"epi_isl_418065_Idaho_20200313_null_1":"test",
"epi_isl_418078_Washington_20200315_null_1":"test",
"epi_isl_418638_Li_ge_20200319_null_1":"test",
"epi_isl_418954_Washington_20200323_null_1":"test",
"epi_isl_418991_Hangzhou_20200204_null_1":"test",
"epi_isl_419431_Wales_20200317_null_1":"test",
"epi_isl_419497_Wales_20200320_null_1":"test",
"epi_isl_419575_Luxembourg_20200314_null_1":"test",
"epi_isl_420084_Taiwan_20200321_null_1":"test",
"epi_isl_420106_Singapore_20200306_null_1":"test",
"epi_isl_420107_Singapore_20200309_null_14":"test",
"epi_isl_420388_Vilvoorde_20200324_null_1":"test",
"epi_isl_421520_Comunitat_Valenciana_20200320_null_4456":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":0
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":2
}
}
}