{
"MLE":{
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[0.6647206207425062, 2.335279379257495, 0, 1, 0.221573540247502, 0, 0.4282142894260264, 10.41424412176031, 0.778426459752498, 1, 0.04111813439549426],
[0.6437517271268426, 2.213650500131196, 0, 0, 0.2252926525309621, 0, 0, 0, 1, 1, 0.04111813439549426],
[0.6437517271268426, 2.356248272873158, 0, 0, 0.2145839090422808, 0, 0, 0, 1, 1, 0.04111813439549426],
[0.4046612010734646, 1.694882990266451, 0, 0, 0.1927376440765519, 0, 0, 0, 1, 1, 0.04111813439549426],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.04111813439549426],
[0.9941407952902355, 2, 0, 1, 0.3320287398822435, 0, 0.4999999999999999, 12.16008477405021, 0.6679712601177565, 1, 0.04111813439549426],
[0.4046612010734646, 2.00012758146795, 0, 0, 0.1682730741307821, 0, 0, 0, 1, 1, 0.04111813439549426],
[1, 2, 0, 1, 0.3333333333333333, 0, 0.4999999999999999, 12.16008477405021, 0.6666666666666667, 1, 0.04111813439549426],
[0, 3, 0, 0, 0, null, 0, null, 1, 1, 0.04111813439549426],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.04111813439549426],
[0.4047887825414139, 1.694755408798502, 0, 0, 0.1927984103459524, 0, 0, 0, 1, 1, 0.04111813439549426]
]
}
}
},
"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":{
"Node18":{
"amino-acid": [
["A", "G", "N", "A", "T", "E", "V", "P", "A", "N", "S", "T", "V", "L", "S", "F", "C", "A", "F", "A", "V", "D", "A", "A", "K", "A", "Y", "K", "D", "Y", "L", "A", "S", "G", "G", "Q", "P", "I", "T", "N", "C", "V", "K", "M", "L", "C", "T", "H", "T", "G", "T", "G", "Q", "A", "I", "T", "V", "T", "P", "E", "A", "N", "M", "D", "Q", "E", "S", "F", "G", "G", "A", "S", "C", "C", "L", "Y", "C", "R", "C", "H", "I", "D", "H", "P", "N", "P", "K", "G", "F", "C", "D", "L", "K", "G", "K", "Y", "V", "Q", "I", "P", "T", "T", "C", "A", "N", "D", "P", "V", "G", "F", "T", "L", "K", "N", "T", "V", "C", "T", "V", "C", "G", "M", "W", "K", "G", "Y", "G", "C", "S", "C", "D", "Q", "L", "R", "E", "P", "M", "L", "Q"]
],
"codon": [
["GCT", "GGT", "AAT", "GCA", "ACA", "GAA", "GTG", "CCT", "GCC", "AAT", "TCA", "ACT", "GTA", "TTA", "TCT", "TTC", "TGT", "GCT", "TTT", "GCT", "GTA", "GAT", "GCT", "GCT", "AAA", "GCT", "TAC", "AAA", "GAT", "TAT", "CTA", "GCT", "AGT", "GGG", "GGA", "CAA", "CCA", "ATC", "ACT", "AAT", "TGT", "GTT", "AAG", "ATG", "TTG", "TGT", "ACA", "CAC", "ACT", "GGT", "ACT", "GGT", "CAG", "GCA", "ATA", "ACA", "GTT", "ACA", "CCG", "GAA", "GCC", "AAT", "ATG", "GAT", "CAA", "GAA", "TCC", "TTT", "GGT", "GGT", "GCA", "TCG", "TGT", "TGT", "CTG", "TAC", "TGC", "CGT", "TGC", "CAC", "ATA", "GAT", "CAT", "CCA", "AAT", "CCT", "AAA", "GGA", "TTT", "TGT", "GAC", "TTA", "AAA", "GGT", "AAG", "TAT", "GTA", "CAA", "ATA", "CCT", "ACA", "ACT", "TGT", "GCT", "AAT", "GAC", "CCT", "GTG", "GGT", "TTT", "ACA", "CTT", "AAA", "AAC", "ACA", "GTC", "TGT", "ACC", "GTC", "TGC", "GGT", "ATG", "TGG", "AAA", "GGT", "TAT", "GGC", "TGT", "AGT", "TGT", "GAT", "CAA", "CTC", "CGC", "GAA", "CCC", "ATG", "CTT", "CAG"]
],
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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": [
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]
},
"Node26":{
"Global MG94xREV":0.002416396373448084,
"Nucleotide GTR":0.002403603520204966,
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],
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],
"nonsynonymous substitution count": [
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],
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]
},
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"Nucleotide GTR":0.002401703399158888,
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],
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],
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]
},
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"Nucleotide GTR":0.002400544556190559,
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]
},
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"Nucleotide GTR":0.002422260937127293,
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"Nucleotide GTR":0.002403763037985081,
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"Nucleotide GTR":0.002405070247016329,
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]
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"Nucleotide GTR":0.002408367595465677,
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]
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"Nucleotide GTR":0.004814828275664916,
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"synonymous substitution count": [
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]
},
"epi_isl_418398_Finland_20200313_null_1":{
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"Nucleotide GTR":0.002403758874533929,
"amino-acid": [
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"Nucleotide GTR":0.002422761826554306,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.002404307056494101,
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},
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"Nucleotide GTR":0.002400551009566754,
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"Nucleotide GTR":0,
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"Nucleotide GTR":{
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"amino-acid":{
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"original name":{
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"synonymous substitution count":{
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}
}
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],
"name":"slac.filter.default"
}
},
"fits":{
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"Equilibrium frequencies": [
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[0.01255030123886465],
[0.009973407163291346],
[0.03568436610036532],
[0.02127020621739473],
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[0.008417460659973831],
[0.03011726513397478],
[0.0189240773760415],
[0.009423987700963712],
[0.007489004817868709],
[0.02679529525595284],
[0.01690620349067466],
[0.008419108134054502],
[0.006690452426168184],
[0.02393811360988036],
[0.01594858028407123],
[0.007942222041176145],
[0.006311483102303789],
[0.02258217978785016],
[0.01346044986689392],
[0.00670315976173531],
[0.005326831628339867],
[0.0190591446702708],
[0.01197574636531324],
[0.005963793331317509],
[0.00473927581489127],
[0.01695689852627818],
[0.01069877283745519],
[0.005327874201319332],
[0.004233926956271237],
[0.01514878487122031],
[0.03067976702236268],
[0.01527819514483811],
[0.01214119549798758],
[0.04344060740254767],
[0.02589343117549771],
[0.01289465119406969],
[0.01024705336863388],
[0.03666345892326337],
[0.02303735516657075],
[0.01147235595365701],
[0.009116791292125323],
[0.03261943614678022],
[0.02058088257587012],
[0.01024905893248621],
[0.008144668070413594],
[0.02914122650685814],
[0.01285691559984626],
[0.03655616502380589],
[0.02178985515355712],
[0.01085111431814792],
[0.008623106267375932],
[0.03085305512242311],
[0.009654223606208876],
[0.007671967472144147],
[0.02744992674055621],
[0.01731923618855651],
[0.008624793990626952],
[0.006853905777309657],
[0.02452294175606616]
],
"Log Likelihood":-677.3492900917333,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.8777825686789671, 1]
]
},
"display order":1,
"estimated parameters":33
},
"Nucleotide GTR":{
"AIC-c":1481.788146893293,
"Equilibrium frequencies": [
[0.277707186220528],
[0.2013271212762953],
[0.2236340533672173],
[0.2973316391359593]
],
"Log Likelihood":-701.6727654596979,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.5440593804541283,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.7381562093768191,
"Substitution rate from nucleotide C to nucleotide G":0,
"Substitution rate from nucleotide C to nucleotide T":4.596621846039666,
"Substitution rate from nucleotide G to nucleotide T":1.373373400098622
},
"display order":0,
"estimated parameters":39
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-05/sequences.nsp10.compressed.fas",
"number of sequences":17,
"number of sites":139,
"partition count":1,
"trees":{
"0":"((epi_isl_419245_Hong_Kong_20200222_null_2,epi_isl_416469_Kessel_Lo_20200303_null_1,epi_isl_418986_Hoegaarden_20200302_null_1)Node26,epi_isl_417361_Connecticut_20200314_null_1,epi_isl_420052_Ile_de_France_20200320_null_1,epi_isl_417563_Reykjavik_20200316_null_1,epi_isl_418398_Finland_20200313_null_1,epi_isl_419496_Wales_20200320_null_2,epi_isl_416355_Shanghai_20200204_null_2,epi_isl_417538_Reykjavik_20200317_null_1,epi_isl_419768_Victoria_20200312_null_1,epi_isl_416345_Shanghai_20200204_null_1,epi_isl_419249_Hong_Kong_20200225_null_1,epi_isl_418957_Virginia_20200317_null_1,epi_isl_419917_Victoria_20200320_null_2,epi_isl_417919_Kuala_Lumpur_20200314_null_1,epi_isl_420084_Taiwan_20200321_null_2742)"
}
},
"tested":{
"0":{
"Node26":"test",
"epi_isl_416345_Shanghai_20200204_null_1":"test",
"epi_isl_416355_Shanghai_20200204_null_2":"test",
"epi_isl_416469_Kessel_Lo_20200303_null_1":"test",
"epi_isl_417361_Connecticut_20200314_null_1":"test",
"epi_isl_417538_Reykjavik_20200317_null_1":"test",
"epi_isl_417563_Reykjavik_20200316_null_1":"test",
"epi_isl_417919_Kuala_Lumpur_20200314_null_1":"test",
"epi_isl_418398_Finland_20200313_null_1":"test",
"epi_isl_418957_Virginia_20200317_null_1":"test",
"epi_isl_418986_Hoegaarden_20200302_null_1":"test",
"epi_isl_419245_Hong_Kong_20200222_null_2":"test",
"epi_isl_419249_Hong_Kong_20200225_null_1":"test",
"epi_isl_419496_Wales_20200320_null_2":"test",
"epi_isl_419768_Victoria_20200312_null_1":"test",
"epi_isl_419917_Victoria_20200320_null_2":"test",
"epi_isl_420052_Ile_de_France_20200320_null_1":"test",
"epi_isl_420084_Taiwan_20200321_null_2742":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}