{
"MLE":{
"content":{
"0":{
"by-branch":{
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],
"NAMES": [
["epi_isl_418897_Washington_20200324_null_1"],
["epi_isl_417335_ARA_20200306_null_5"],
["epi_isl_417707_Reykjavik_20200305_null_1"],
["epi_isl_415537_Wales_20200308_null_1"],
["epi_isl_416367_Shanghai_20200201_null_7"],
["epi_isl_418307_Derbyshire_20200324_null_1"],
["epi_isl_418836_British_Columbia_20200310_null_3"],
["epi_isl_419246_Hong_Kong_20200223_null_1"],
["epi_isl_418385_Finland_20200313_null_1"],
["epi_isl_412978_Hubei_20200117_null_1"],
["epi_isl_416412_Victoria_20200302_null_2"],
["epi_isl_417285_England_20200306_null_1"],
["epi_isl_417919_Kuala_Lumpur_20200314_null_1"],
["epi_isl_413870_Guangdong_20200228_null_1"],
["epi_isl_417980_Madrid_20200303_null_1"],
["epi_isl_414008_England_20200227_null_1"],
["epi_isl_417554_Reykjavik_20200316_null_1"],
["epi_isl_417456_Washington_20200314_null_2"],
["epi_isl_418697_England_20200316_null_2"],
["epi_isl_418081_Washington_20200315_null_2"],
["epi_isl_417445_Lombardy_20200224_null_1"],
["epi_isl_419310_Chiba_20200313_null_2858"]
],
"RESOLVED": [
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},
"by-site":{
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[0.6255900594972726, 2.374409940502727, 0, 0, 0.2085300198324243, 0, 0, 0, 1, 1, 0.03753322737805379],
[0.9999999999999998, 2, 0, 0, 0.3333333333333334, 0, 0, 0, 1, 1, 0.03753322737805379],
[0.9999999999999998, 2, 0, 0, 0.3333333333333334, 0, 0, 0, 1, 1, 0.03753322737805379],
[0.9999999999999998, 2, 0, 0, 0.3333333333333334, 0, 0, 0, 1, 1, 0.03753322737805379],
[0.5592630764662944, 2.110042213584897, 0, 0, 0.2095163406563994, 0, 0, 0, 1, 1, 0.03753322737805379],
[1.184853135963567, 1.440736923533705, 0, 0, 0.4512711844248959, 0, 0, 0, 1, 1, 0.03753322737805379],
[0.6285282421529699, 1.462051155843404, 0, 0, 0.3006478695596809, 0, 0, 0, 1, 1, 0.03753322737805379]
]
}
}
},
"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":{
"Node22":{
"amino-acid": [
["A", "I", "A", "S", "E", "F", "S", "S", "L", "P", "S", "Y", "A", "A", "F", "A", "T", "A", "Q", "E", "A", "Y", "E", "Q", "A", "V", "A", "N", "G", "D", "S", "E", "V", "V", "L", "K", "K", "L", "K", "K", "S", "L", "N", "V", "A", "K", "S", "E", "F", "D", "R", "D", "A", "A", "M", "Q", "R", "K", "L", "E", "K", "M", "A", "D", "Q", "A", "M", "T", "Q", "M", "Y", "K", "Q", "A", "R", "S", "E", "D", "K", "R", "A", "K", "V", "T", "S", "A", "M", "Q", "T", "M", "L", "F", "T", "M", "L", "R", "K", "L", "D", "N", "D", "A", "L", "N", "N", "I", "I", "N", "N", "A", "R", "D", "G", "C", "V", "P", "L", "N", "I", "I", "P", "L", "T", "T", "A", "A", "K", "L", "M", "V", "V", "I", "P", "D", "Y", "N", "T", "Y", "K", "N", "T", "C", "D", "G", "T", "T", "F", "T", "Y", "A", "S", "A", "L", "W", "E", "I", "Q", "Q", "V", "V", "D", "A", "D", "S", "K", "I", "V", "Q", "L", "S", "E", "I", "S", "M", "D", "N", "S", "P", "N", "L", "A", "W", "P", "L", "I", "V", "T", "A", "L", "R", "A", "N", "S", "A", "V", "K", "L", "Q"]
],
"codon": [
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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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_412978_Hubei_20200117_null_1":{
"Global MG94xREV":0.001708700390012006,
"Nucleotide GTR":0.001689085735813713,
"amino-acid": [
["A", "I", "A", "S", "E", "F", "S", "S", "L", "P", "S", "Y", "A", "A", "F", "A", "N", "A", "Q", "E", "A", "Y", "E", "Q", "A", "V", "A", "N", "G", "D", "S", "E", "V", "V", "L", "K", "K", "L", "K", "K", "S", "L", "N", "V", "A", "K", "S", "E", "F", "D", "R", "D", "A", "A", "M", "Q", "R", "K", "L", "E", "K", "M", "A", "D", "Q", "A", "M", "T", "Q", "M", "Y", "K", "Q", "A", "R", "S", "E", "D", "K", "R", "A", "K", "V", "T", "S", "A", "M", "Q", "T", "M", "L", "F", "T", "M", "L", "R", "K", "L", "D", "N", "D", "A", "L", "N", "N", "I", "I", "N", "N", "A", "R", "D", "G", "C", "V", "P", "L", "N", "I", "I", "P", "L", "T", "T", "A", "A", "K", "L", "M", "V", "V", "I", "P", "D", "Y", "N", "T", "Y", "K", "N", "T", "C", "D", "G", "T", "T", "F", "T", "Y", "A", "S", "A", "L", "W", "E", "I", "Q", "Q", "V", "V", "D", "A", "D", "S", "K", "I", "V", "Q", "L", "S", "E", "I", "S", "M", "D", "N", "S", "P", "N", "L", "A", "W", "P", "L", "I", "V", "T", "A", "L", "R", "A", "N", "S", "A", "V", "K", "L", "Q"]
],
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],
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],
"original name":"epi_isl_412978_Hubei_20200117_null_1",
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]
},
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"Nucleotide GTR":0.001685063934701808,
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]
},
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"Nucleotide GTR":0.001684910532003326,
"amino-acid": [
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"Nucleotide GTR":0.001691733582234564,
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"Nucleotide GTR":0.001684910618202654,
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},
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"Nucleotide GTR":0.001684896080666131,
"amino-acid": [
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]
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"Global MG94xREV":0.001703123151714436,
"Nucleotide GTR":0.001683572520209196,
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"Nucleotide GTR":0.001684020856691674,
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]
},
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"Global MG94xREV":0.001704472042277337,
"Nucleotide GTR":0.001684905926476489,
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"Nucleotide GTR":0.001684942475280892,
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"Nucleotide GTR":0.001684942489900116,
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"Nucleotide GTR":0.001684020808934528,
"amino-acid": [
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"Nucleotide GTR":0.001684910581030574,
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]
},
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"Nucleotide GTR":0.001685009660310856,
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],
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]
},
"epi_isl_419246_Hong_Kong_20200223_null_1":{
"Global MG94xREV":0.001703122398583771,
"Nucleotide GTR":0.00168357177572393,
"amino-acid": [
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],
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"original name":"epi_isl_419246_Hong_Kong_20200223_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419310_Chiba_20200313_null_2858":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["A", "I", "A", "S", "E", "F", "S", "S", "L", "P", "S", "Y", "A", "A", "F", "A", "T", "A", "Q", "E", "A", "Y", "E", "Q", "A", "V", "A", "N", "G", "D", "S", "E", "V", "V", "L", "K", "K", "L", "K", "K", "S", "L", "N", "V", "A", "K", "S", "E", "F", "D", "R", "D", "A", "A", "M", "Q", "R", "K", "L", "E", "K", "M", "A", "D", "Q", "A", "M", "T", "Q", "M", "Y", "K", "Q", "A", "R", "S", "E", "D", "K", "R", "A", "K", "V", "T", "S", "A", "M", "Q", "T", "M", "L", "F", "T", "M", "L", "R", "K", "L", "D", "N", "D", "A", "L", "N", "N", "I", "I", "N", "N", "A", "R", "D", "G", "C", "V", "P", "L", "N", "I", "I", "P", "L", "T", "T", "A", "A", "K", "L", "M", "V", "V", "I", "P", "D", "Y", "N", "T", "Y", "K", "N", "T", "C", "D", "G", "T", "T", "F", "T", "Y", "A", "S", "A", "L", "W", "E", "I", "Q", "Q", "V", "V", "D", "A", "D", "S", "K", "I", "V", "Q", "L", "S", "E", "I", "S", "M", "D", "N", "S", "P", "N", "L", "A", "W", "P", "L", "I", "V", "T", "A", "L", "R", "A", "N", "S", "A", "V", "K", "L", "Q"]
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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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_419310_Chiba_20200313_null_2858",
"synonymous substitution count": [
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]
}
},
"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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":1949.800786340028,
"Equilibrium frequencies": [
[0.03809192095363614],
[0.01359662678130916],
[0.02394679889511921],
[0.05185501367658157],
[0.02903266716397035],
[0.01036299377957186],
[0.01825162461118054],
[0.03952253693605372],
[0.01036220539488282],
[0.003698711849081503],
[0.006514285509602039],
[0.01410620123687681],
[0.02825356528790226],
[0.01008489918186414],
[0.01776183581928104],
[0.03846193570021333],
[0.01515647321817618],
[0.005409989953493742],
[0.009528241344317902],
[0.02063269864950838],
[0.01155186798950173],
[0.004123353029934661],
[0.007262176668492659],
[0.01572570397052912],
[0.004123039337920032],
[0.001471688108105334],
[0.002591982535667098],
[0.005612745587631448],
[0.01124186953252631],
[0.00401270139523746],
[0.007067293592996859],
[0.01530369915103615],
[0.03590065542962861],
[0.01281447091300984],
[0.02256924183011623],
[0.04887201620961908],
[0.02736254181891812],
[0.009766855007197537],
[0.01720168659896303],
[0.03724897418465822],
[0.009766111974912509],
[0.003485940753394432],
[0.006139546486382204],
[0.01329473172651257],
[0.02662825834627987],
[0.009504758003969537],
[0.01674007326440108],
[0.03624938480814742],
[0.008294842569229495],
[0.03163499166306243],
[0.01771184922285445],
[0.006322112339335424],
[0.01113469945284767],
[0.0241113643180811],
[0.002256459119643551],
[0.003974145471687284],
[0.008605716726049407],
[0.01723654549411932],
[0.006152456222090982],
[0.01083589586087408],
[0.02346432734181284]
],
"Log Likelihood":-937.574779459963,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.9584077001540696, 1]
]
},
"display order":1,
"estimated parameters":37
},
"Nucleotide GTR":{
"AIC-c":2058.676024480944,
"Equilibrium frequencies": [
[0.3249119583524728],
[0.1796049609554433],
[0.2036441586280815],
[0.2918389220640025]
],
"Log Likelihood":-980.1498112879448,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.2230985766040485,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.4126100908486309,
"Substitution rate from nucleotide C to nucleotide G":0,
"Substitution rate from nucleotide C to nucleotide T":2.493759923368734,
"Substitution rate from nucleotide G to nucleotide T":0.6579963541068161
},
"display order":0,
"estimated parameters":49
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-02/sequences.nsp8.compressed.fas",
"number of sequences":22,
"number of sites":198,
"partition count":1,
"trees":{
"0":"(epi_isl_418897_Washington_20200324_null_1,epi_isl_417335_ARA_20200306_null_5,epi_isl_417707_Reykjavik_20200305_null_1,epi_isl_415537_Wales_20200308_null_1,epi_isl_416367_Shanghai_20200201_null_7,epi_isl_418307_Derbyshire_20200324_null_1,epi_isl_418836_British_Columbia_20200310_null_3,epi_isl_419246_Hong_Kong_20200223_null_1,epi_isl_418385_Finland_20200313_null_1,epi_isl_412978_Hubei_20200117_null_1,epi_isl_416412_Victoria_20200302_null_2,epi_isl_417285_England_20200306_null_1,epi_isl_417919_Kuala_Lumpur_20200314_null_1,epi_isl_413870_Guangdong_20200228_null_1,epi_isl_417980_Madrid_20200303_null_1,epi_isl_414008_England_20200227_null_1,epi_isl_417554_Reykjavik_20200316_null_1,epi_isl_417456_Washington_20200314_null_2,epi_isl_418697_England_20200316_null_2,epi_isl_418081_Washington_20200315_null_2,epi_isl_417445_Lombardy_20200224_null_1,epi_isl_419310_Chiba_20200313_null_2858)"
}
},
"tested":{
"0":{
"epi_isl_412978_Hubei_20200117_null_1":"test",
"epi_isl_413870_Guangdong_20200228_null_1":"test",
"epi_isl_414008_England_20200227_null_1":"test",
"epi_isl_415537_Wales_20200308_null_1":"test",
"epi_isl_416367_Shanghai_20200201_null_7":"test",
"epi_isl_416412_Victoria_20200302_null_2":"test",
"epi_isl_417285_England_20200306_null_1":"test",
"epi_isl_417335_ARA_20200306_null_5":"test",
"epi_isl_417445_Lombardy_20200224_null_1":"test",
"epi_isl_417456_Washington_20200314_null_2":"test",
"epi_isl_417554_Reykjavik_20200316_null_1":"test",
"epi_isl_417707_Reykjavik_20200305_null_1":"test",
"epi_isl_417919_Kuala_Lumpur_20200314_null_1":"test",
"epi_isl_417980_Madrid_20200303_null_1":"test",
"epi_isl_418081_Washington_20200315_null_2":"test",
"epi_isl_418307_Derbyshire_20200324_null_1":"test",
"epi_isl_418385_Finland_20200313_null_1":"test",
"epi_isl_418697_England_20200316_null_2":"test",
"epi_isl_418836_British_Columbia_20200310_null_3":"test",
"epi_isl_418897_Washington_20200324_null_1":"test",
"epi_isl_419246_Hong_Kong_20200223_null_1":"test",
"epi_isl_419310_Chiba_20200313_null_2858":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":0
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":2
}
}
}