{
"MLE":{
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"NAMES": [
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[0.004918661157847962, 0.003944183153809629, 0, 0, 0.554975466665739, 0, 0, 0, 1, 1, 2519.010945249385],
[0.002427875959977528, 0.007224576567542569, 0, 0, 0.2515294380423435, 0, 0, 0, 1, 1, 2519.010945249385],
[0.9085116759364483, 2.09642817557267, 1, 2, 0.3023393880846508, 1.100701318966815, 0.954003587293741, -5.81472479946098e-05, 0.781045829335117, 0.6604274205404091, 2522.866287441022],
[0.772776257031248, 2.210559700128677, 2.010416666666667, 5.989583333333334, 0.2590309197918545, 2.601550770193207, 2.709532492148789, 4.275326523098434e-05, 0.658181686363118, 0.651773344702166, 2525.695321098541],
[0.002187782840441418, 0.007450103576830375, 2, 1, 0.2269981970861113, 914.1675138088525, 134.2263217802735, -0.3091547565678106, 0.9883031957048357, 0.1311909358507066, 2522.818023851124],
[0.002601502777615958, 0.007036383639655834, 2, 0, 0.2699246146908182, 768.7864173002416, 0, -0.3047332031212764, 0.9999999999999999, 0.07285929761598675, 2522.818023851124],
[0.002787636807816789, 0.006842516382637866, 0.75, 1, 0.28946962241264, 269.0450914900146, 146.1450647801721, -0.04873426852528275, 0.8439105793421027, 0.4501178299523207, 2521.839978906904],
[0, 0.00680316915584486, 0, 0, 0, null, 0, null, 1, 1, 2519.010945249385],
[0.002797840312111579, 0.006854612215408517, 0, 1, 0.2898579717574015, 0, 145.8871732746741, 0.05791446581437188, 0.7101420282425985, 1, 2519.010945249385],
[0.003217484175840032, 0.00602322112573788, 1, 0, 0.3481859956393832, 310.8018393715694, 0, -0.123382488654014, 1, 0.3481859956393832, 2519.010945249385],
[0.003066398102025798, 0.006134020231393964, 0, 1, 0.3332889865330752, 0, 163.0252203737431, 0.06470852888278629, 0.6667110134669247, 1, 2519.377633650871],
[0.002374139187295787, 0.005385761878553176, 0, 0, 0.3059496721864516, 0, 0, 0, 1, 1, 2519.377633650871],
[590.2921244025989, 1177.083709714609, 2, 2, 0.3339935473868497, 0.0033881529454998, 0.001699114500943108, -0.0003938251737515621, 0.8883011601878072, 0.408581120129792, 4.2888026391685],
[456.0658085747724, 1310.096261467874, 0, 1, 0.258224211871881, 0, 0.0007633026895898227, 0.0001779757087954529, 0.741775788128119, 1, 4.2888026391685],
[0.002313857253127509, 0.006885293634085881, 0, 0, 0.2515294380423435, 0, 0, 0, 1, 1, 2519.724749994906],
[0.002314176053159547, 0.006886242280260216, 0, 0, 0.2515294380423435, 0, 0, 0, 1, 1, 2519.377633650871],
[0.002314176053159547, 0.006886242280260216, 0, 0, 0.2515294380423435, 0, 0, 0, 1, 1, 2519.377633650871],
[0.002374139187295787, 0.005385761878553176, 0, 0, 0.3059496721864516, 0, 0, 0, 1, 1, 2519.377633650871],
[0.003066806111139921, 0.006133612222279841, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 2519.377633650871],
[0.002314176053159547, 0.006886242280260216, 0, 1, 0.2515294380423435, 0, 145.2170805646142, 0.05764006103133405, 0.7484705619576566, 1, 2519.377633650871],
[0.002666707569186823, 0.006533710764232939, 0, 0, 0.2898463387800777, 0, 0, 0, 1, 1, 2519.377633650871],
[0.003066806111139921, 0.006133612222279841, 0, 1, 0.3333333333333333, 0, 163.0360648440706, 0.06471283330709433, 0.6666666666666667, 1, 2519.377633650871],
[0, 0, 0, 0, null, null, null, null, 1, 1, 2527.020482386796]
]
}
}
},
"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":{
"Node12":{
"Global MG94xREV":3.479657175950207,
"Nucleotide GTR":3.250414029576016,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "I", "F", "-", "-", "-", "-", "-", "-", "-", "-", "P", "K", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "ATT", "TTT", "---", "---", "---", "---", "---", "---", "---", "---", "CCA", "AAA", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
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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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"Node22":{
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["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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],
"nonsynonymous substitution count": [
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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]
]
},
"Node26":{
"Global MG94xREV":0.00665977170743038,
"Nucleotide GTR":0.006221019570898928,
"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", "V", "-"]
],
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],
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],
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"Nucleotide GTR":0.008403908643729899,
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],
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],
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],
"synonymous substitution count": [
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]
},
"Node9":{
"Global MG94xREV":0.003971664102206212,
"Nucleotide GTR":0.003710007068454731,
"amino-acid": [
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],
"codon": [
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],
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},
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"Global MG94xREV":0.9780449442198705,
"Nucleotide GTR":0.9136104068585557,
"amino-acid": [
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],
"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_413752_China_20200201_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
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],
"original name":"epi_isl_413752_China_20200201_null_1",
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]
},
"epi_isl_413875_Guangdong_20200210_null_1":{
"Global MG94xREV":0.001708686864706565,
"Nucleotide GTR":0.001596116938065267,
"amino-acid": [
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"Global MG94xREV":0.008377180840349968,
"Nucleotide GTR":0.007825284145796143,
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"Global MG94xREV":0.00837044042002969,
"Nucleotide GTR":0.007818987790820225,
"amino-acid": [
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"Nucleotide GTR":0.007758885989157366,
"amino-acid": [
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"Nucleotide GTR":0.007823746298134105,
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"Nucleotide GTR":0.007817683829810199,
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"Nucleotide GTR":0.007825169659354703,
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"epi_isl_417518_Taoyuan_20200204_null_4":{
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"Nucleotide GTR":0.002568935977620697,
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"original name":"epi_isl_417518_Taoyuan_20200204_null_4",
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"Nucleotide GTR":0.007817843388128156,
"amino-acid": [
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"original name":"epi_isl_417576_Reykjavik_20200317_null_2",
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"Nucleotide GTR":0.007821476207730046,
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"original name":"epi_isl_418004_Portugal_20200312_null_1",
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"Nucleotide GTR":2352.967032751422,
"amino-acid": [
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"original name":"epi_isl_418035_Washington_20200314_null_1",
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"epi_isl_418052_Washington_20200316_null_1":{
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"Nucleotide GTR":0.3242479869409375,
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"original name":"epi_isl_418052_Washington_20200316_null_1",
"synonymous substitution count": [
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"epi_isl_418065_Washington_20200313_null_1":{
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"Nucleotide GTR":2.64265421148298,
"amino-acid": [
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],
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"original name":"epi_isl_418065_Washington_20200313_null_1",
"synonymous substitution count": [
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"epi_isl_418078_Washington_20200315_null_1":{
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"Nucleotide GTR":0.350934527151582,
"amino-acid": [
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"original name":"epi_isl_418078_Washington_20200315_null_1",
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"epi_isl_418638_Li_ge_20200319_null_1":{
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"Nucleotide GTR":0.004050514422336212,
"amino-acid": [
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"original name":"epi_isl_418638_Li_ge_20200319_null_1",
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"epi_isl_418738_England_20200317_null_2709":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_418738_England_20200317_null_2709",
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]
}
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"attributes":{
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"display order":1
},
"Nucleotide GTR":{
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"display order":0
},
"amino-acid":{
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"codon":{
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"nonsynonymous substitution count":{
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"original name":{
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"display order":-1
},
"synonymous substitution count":{
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}
}
},
"data partitions":{
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"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"
}
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"fits":{
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"Equilibrium frequencies": [
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[0.0112154489059479],
[0.008115116865856174],
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[0.006351574661431973],
[0.03328888850372889],
[0.02611467788247733],
[0.01889569153296247],
[0.0498310796944817],
[0.01178298358724767],
[0.009243589519097994],
[0.0066883465687853],
[0.01763828173803812],
[0.005299915541892007],
[0.004157711278504879],
[0.003008378282715179],
[0.007933593628770727],
[0.003348090296801778],
[0.002626531060435745],
[0.001900468424044393],
[0.005011851158249444],
[0.02626733736081694],
[0.02060636701436449],
[0.01491006538432965],
[0.03932032099065381],
[0.02191297559623337],
[0.04181354402275905],
[0.01256404989551184],
[0.009856325358652678],
[0.00713170135445489],
[0.01880748200885602],
[0.006226489277911356],
[0.004505275587092564],
[0.01188116065688202],
[0.06226969743478813],
[0.04884972624323763],
[0.03534599824343367],
[0.09321327310392498]
],
"Log Likelihood":-261.8317067294672,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.3083543463678816, 1]
]
},
"display order":1,
"estimated parameters":37
},
"Nucleotide GTR":{
"AIC-c":628.160450290466,
"Equilibrium frequencies": [
[0.2257546563904946],
[0.1872190109184329],
[0.1287732819524727],
[0.4582530507385999]
],
"Log Likelihood":-272.3424359421481,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.2006753786506494,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0,
"Substitution rate from nucleotide C to nucleotide G":0.2383067906677128,
"Substitution rate from nucleotide C to nucleotide T":1.105261205094276,
"Substitution rate from nucleotide G to nucleotide T":0.522605856437111
},
"display order":0,
"estimated parameters":41
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-03-31/sequences.ORF7b.compressed.fas",
"number of sequences":18,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_416633_unknown_20200217_null_1,epi_isl_418738_England_20200317_null_2709,epi_isl_417253_England_20200303_null_1,epi_isl_417348_Washington_20200313_null_1,((epi_isl_418078_Washington_20200315_null_1,epi_isl_417518_Taoyuan_20200204_null_4)Node27,epi_isl_413875_Guangdong_20200210_null_1)Node26,epi_isl_414509_North_Rhine_Westphalia_20200228_null_1,epi_isl_418004_Portugal_20200312_null_1,epi_isl_417456_Washington_20200314_null_1,(epi_isl_418638_Li_ge_20200319_null_1,epi_isl_418052_Washington_20200316_null_1,(epi_isl_413752_China_20200201_null_1,epi_isl_418035_Washington_20200314_null_1)Node12,epi_isl_413747_China_20200201_null_1,epi_isl_418065_Washington_20200313_null_1)Node9,epi_isl_417453_Washington_20200314_null_1,epi_isl_417576_Reykjavik_20200317_null_2)"
}
},
"tested":{
"0":{
"Node12":"test",
"Node26":"test",
"Node27":"test",
"Node9":"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_417348_Washington_20200313_null_1":"test",
"epi_isl_417453_Washington_20200314_null_1":"test",
"epi_isl_417456_Washington_20200314_null_1":"test",
"epi_isl_417518_Taoyuan_20200204_null_4":"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_Washington_20200316_null_1":"test",
"epi_isl_418065_Washington_20200313_null_1":"test",
"epi_isl_418078_Washington_20200315_null_1":"test",
"epi_isl_418638_Li_ge_20200319_null_1":"test",
"epi_isl_418738_England_20200317_null_2709":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":0
},
"Total time":{
"order":0,
"timer":2
}
}
}