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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":{
"Node11":{
"Global MG94xREV":1902.631756999873,
"Nucleotide GTR":1681.296761835987,
"amino-acid": [
["Y", "K", "P", "H", "S", "V", "D", "D", "V", "L", "L", "C", "P", "I", "H", "F", "Y", "S", "K", "-", "-", "-", "-", "-", "-", "-", "-", "-", "W", "Y", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
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],
"nonsynonymous substitution count": [
[3, 2, 2.5, 1, 0, 1.5, 2, 0, 1, 2, 0, 0, 2, 1.5, 2, 0, 2.25, 1.833333333333333, 2.75, 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": [
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]
},
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"Nucleotide GTR":0.0242472171339809,
"amino-acid": [
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],
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],
"nonsynonymous substitution count": [
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],
"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]
]
},
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"Global MG94xREV":0.5711720295035558,
"Nucleotide GTR":0.5047270340792908,
"amino-acid": [
["Y", "K", "P", "H", "S", "L", "S", "D", "G", "L", "L", "L", "P", "V", "H", "F", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
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],
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],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0.75, 1, 0, 0, 0.5, 0, 1, 0.5, 0, 0, 0, 0, 0, 0, 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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"Nucleotide GTR":0.0164745707786576,
"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", "-", "-"]
],
"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", "---", "---"]
],
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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, 1, 0, 0, 0, 0]
]
},
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"Global MG94xREV":0.2931015852570664,
"Nucleotide GTR":0.2590047939485395,
"amino-acid": [
["-", "-", "-", "-", "-", "L", "I", "D", "-", "-", "L", "C", "F", "I", "A", "F", "L", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
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],
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],
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"Nucleotide GTR":0.137466445196527,
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],
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],
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],
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["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", "---", "---", "---", "---"]
],
"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_485935_CT_20200327_null_3",
"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_485971_WA_20200317_null_5":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"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", "-", "-", "-", "-", "-", "-"]
],
"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", "---", "---", "---", "---", "---", "---"]
],
"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_485971_WA_20200317_null_5",
"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_486362_California_20200521_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"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", "Y"]
],
"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", "CAC", "GCC", "TAN"]
],
"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, 4]
],
"original name":"epi_isl_486362_California_20200521_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]
]
}
},
"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":inf,
"Equilibrium frequencies": [
[0.0141159109070893],
[0.01139509661927142],
[0.009805338781365962],
[0.02323552557562964],
[0.007045929569245452],
[0.005687840391073211],
[0.004894315847615497],
[0.01159796755504219],
[0.003836131613423541],
[0.003096724729060822],
[0.002664693077698232],
[0.006314472711103533],
[0.02919113377056918],
[0.02356459968691473],
[0.0202770446708369],
[0.04805012866488444],
[0.0144536152285462],
[0.01166770909161383],
[0.01003991842001707],
[0.02379140450188949],
[0.00721449402674852],
[0.005823914378254432],
[0.005011405819576474],
[0.01187543344365783],
[0.003927905940426408],
[0.003170809733581578],
[0.002728442301791382],
[0.006465538039887266],
[0.02988949267120498],
[0.02412835127192059],
[0.02076214589149403],
[0.04919966383859697],
[0.01089521815993089],
[0.008795186115697382],
[0.00756814815977339],
[0.01793409733692768],
[0.005438327026977985],
[0.004390100102465687],
[0.00377762648506071],
[0.008951769925136261],
[0.002960878054101814],
[0.00239017458571702],
[0.002056715475315109],
[0.004873759703162457],
[0.02253087121755274],
[0.01818808974711184],
[0.0156506248007332],
[0.0370869891332159],
[0.02149214377226252],
[0.04382422308301976],
[0.013289236271622],
[0.01072776190698446],
[0.009231105569207603],
[0.0218747760100116],
[0.005840692301593779],
[0.005025843013738729],
[0.01190964498919207],
[0.05505701836800519],
[0.04444488549140229],
[0.0382442706633303],
[0.09062672376071854]
],
"Log Likelihood":-inf,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.9165418920175951, 1]
]
},
"display order":1,
"estimated parameters":54
},
"Nucleotide GTR":{
"AIC-c":1022.312087480979,
"Equilibrium frequencies": [
[0.2246563573883162],
[0.1902920962199312],
[0.1327319587628866],
[0.452319587628866]
],
"Log Likelihood":-453.1761978602286,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.4331474683075413,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.13389511951775,
"Substitution rate from nucleotide C to nucleotide G":1.606683512760432,
"Substitution rate from nucleotide C to nucleotide T":1.018044039292995,
"Substitution rate from nucleotide G to nucleotide T":1.031714736398414
},
"display order":0,
"estimated parameters":57
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-07-10/sequences.ORF7b.compressed.fas",
"number of sequences":26,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(((((epi_isl_477216_Karnataka_20200609_null_1,((((epi_isl_460625_Washington_20200331_null_2,epi_isl_470866_Western_Australia_20200331_null_1)Node39,epi_isl_424220_Washington_20200321_null_1)Node38,epi_isl_479738_Karnataka_20200602_null_1)Node37,(epi_isl_449375_England_20200328_null_5,epi_isl_413747_China_20200201_null_1,epi_isl_479752_Karnataka_20200617_null_1)Node31,epi_isl_472891_Wales_20200519_null_2)Node29,epi_isl_430896_Washington_20200329_null_1)Node27,epi_isl_477236_Karnataka_20200616_null_1)Node26,epi_isl_477213_Karnataka_20200527_null_1)Node25,epi_isl_474778_Wales_20200501_null_8)Node24,epi_isl_428830_Singapore_20200227_null_16,(((epi_isl_453320_England_20200410_null_1,(epi_isl_477219_Karnataka_20200611_null_1,epi_isl_479751_Karnataka_20200617_null_1)Node19,epi_isl_450857_Florida_20200410_null_1,epi_isl_449506_England_20200331_null_2,epi_isl_453338_England_20200411_null_6)Node12,epi_isl_449433_England_20200327_null_2)Node11,epi_isl_485935_CT_20200327_null_3,epi_isl_486362_California_20200521_null_1,epi_isl_463896_Zhejiang_20200131_null_1)Node5,epi_isl_478427_England_20200401_null_3,epi_isl_485971_WA_20200317_null_5)"
}
},
"tested":{
"0":{
"Node11":"test",
"Node12":"test",
"Node19":"test",
"Node24":"test",
"Node25":"test",
"Node26":"test",
"Node27":"test",
"Node29":"test",
"Node31":"test",
"Node37":"test",
"Node38":"test",
"Node39":"test",
"Node5":"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_460625_Washington_20200331_null_2":"test",
"epi_isl_463896_Zhejiang_20200131_null_1":"test",
"epi_isl_470866_Western_Australia_20200331_null_1":"test",
"epi_isl_472891_Wales_20200519_null_2":"test",
"epi_isl_474778_Wales_20200501_null_8":"test",
"epi_isl_477213_Karnataka_20200527_null_1":"test",
"epi_isl_477216_Karnataka_20200609_null_1":"test",
"epi_isl_477219_Karnataka_20200611_null_1":"test",
"epi_isl_477236_Karnataka_20200616_null_1":"test",
"epi_isl_478427_England_20200401_null_3":"test",
"epi_isl_479738_Karnataka_20200602_null_1":"test",
"epi_isl_479751_Karnataka_20200617_null_1":"test",
"epi_isl_479752_Karnataka_20200617_null_1":"test",
"epi_isl_485935_CT_20200327_null_3":"test",
"epi_isl_485971_WA_20200317_null_5":"test",
"epi_isl_486362_California_20200521_null_1":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}