{
"MLE":{
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"NAMES": [
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[38.74190450733433, 89.41898080573826, 0, 0, 0.3022911741963646, 0, 0, 0, 1, 1, 0.1503173450459256],
[42.72029510435752, 85.44059020871504, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1503173450459256],
[42.72029510435752, 85.44059020871504, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1503173450459256],
[60.51996892954838, 54.86922434962194, 0, 0, 0.5244855883785198, 0, 0, 0, 1, 1, 0.1503173450459256],
[32.62713824945482, 95.53374706361774, 0, 0, 0.2545795323569509, 0, 0, 0, 1, 1, 0.1503173450459256],
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[2.545899249012849, 4.781712795130073, 1.625, 3.875, 0.3474391430217471, 0.6382813462198397, 0.8103790767079293, 0.06548963749684161, 0.5850951535573788, 0.7294584641043607, 2.627862010938592],
[1.460236766203507, 4.731614721875582, 2, 1, 0.2358320074399135, 1.369640900906661, 0.2113443420016257, -0.3722851405506613, 0.9868837935647987, 0.1406177943290152, 3.111315582437037],
[1.740482274449237, 4.451369213629853, 2, 0, 0.2810923804939627, 1.149106790319302, 0, -0.3693314804855723, 1, 0.0790129263717626, 3.111315582437037],
[2.362273496877414, 6.29469159650931, 0.75, 1, 0.272875479038493, 0.3174907566763087, 0.1588640181442003, -0.07139728929702621, 0.854566426337721, 0.4274474098425087, 2.221747353351066],
[0, 84.28249516870368, 0, 0, 0, null, 0, null, 1, 1, 0.1503173450459256],
[38.74441438328998, 89.41647092978262, 0, 1, 0.3023107579870782, 0, 0.01118362187191759, 0.0744000758428824, 0.6976892420129217, 1, 0.1503173450459256],
[42.72029510435752, 81.46323671393371, 1, 0, 0.3440093422923986, 0.02340807800033195, 0, -0.1557243975615736, 1, 0.3440093422923987, 0.1503173450459256],
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[7.749849561017188, 19.97606011624903, 0, 0, 0.2795165118557554, 0, 0, 0, 1, 1, 0.5545785234693613],
[2.913949417201725, 2.295332373422333, 2, 2, 0.5593764235304771, 0.6863537123168756, 0.8713335040964053, 0.053481694813511, 0.5936029841588122, 0.7708949142533501, 3.458749623110271],
[1.294955944118453, 2.745655201993105, 0.4583333333333334, 2.041666666666667, 0.3204851685281919, 0.3539373948704839, 0.7435990743428367, 0.1126596955352757, 0.5863219604006704, 0.6193749642066987, 3.458749623110271],
[4.520620195352786, 14.82474576504228, 0, 0, 0.2336797455580658, 0, 0, 0, 1, 1, 0.9313652410030818],
[7.591979024699385, 24.8968402632902, 0, 0, 0.2336797455580658, 0, 0, 0, 1, 1, 0.5545785234693613],
[7.591979024699385, 24.8968402632902, 0, 0, 0.2336797455580658, 0, 0, 0, 1, 1, 0.5545785234693613],
[7.749849561017188, 19.97809798171582, 0, 1, 0.2794959687900983, 0, 0.05005481507374783, 0.09025739900747022, 0.7205040312099017, 1, 0.5545785234693613],
[10.82960642932985, 21.65921285865971, 0, 0, 0.3333333333333334, 0, 0, 0, 1, 1, 0.5545785234693613],
[7.591979024699385, 24.21829189406771, 0, 1, 0.2386643937766763, 0, 0.04129110361598006, 0.07445492724397082, 0.7613356062233237, 1, 0.5545785234693613],
[9.819570202498241, 22.66924908549133, 1, 0, 0.3022446003794397, 0.101837451067419, 0, -0.1836303548690254, 1, 0.3022446003794397, 0.5545785234693613],
[10.82960642932985, 21.65921285865971, 0, 1, 0.3333333333333334, 0, 0.04616972955229921, 0.08325192483738497, 0.6666666666666666, 1, 0.5545785234693613],
[0, 0, 0, 0, null, null, null, null, 1, 1, 6.421601339665473]
]
}
}
},
"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":{
"Node10":{
"Global MG94xREV":0.001853479164090438,
"Nucleotide GTR":0.001775488863847198,
"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", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"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]
],
"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]
]
},
"Node30":{
"Global MG94xREV":0.001122053226656472,
"Nucleotide GTR":0.00107483971072856,
"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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],
"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]
],
"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]
]
},
"Node30_1":{
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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]
]
},
"Node31":{
"Global MG94xREV":0.02199986493660893,
"Nucleotide GTR":0.02107415932040423,
"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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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 1.5, 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, 0, 0, 0, 0]
],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0]
]
},
"Node9":{
"Global MG94xREV":0.005360675750682338,
"Nucleotide GTR":0.005135110381833128,
"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", "-"]
],
"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", "GTC", "---"]
],
"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, 1, 0]
],
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]
},
"epi_isl_413747_China_20200201_null_1":{
"Global MG94xREV":0.8895682290859711,
"Nucleotide GTR":0.852137167211958,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "V", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
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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":2.52738438210719,
"Nucleotide GTR":2.421037642090097,
"amino-acid": [
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],
"codon": [
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],
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"synonymous substitution count": [
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},
"epi_isl_413875_Guangdong_20200210_null_1":{
"Global MG94xREV":0.00278708983504898,
"Nucleotide GTR":0.002669815264472931,
"amino-acid": [
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"Nucleotide GTR":0.007805950634195158,
"amino-acid": [
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"original name":"epi_isl_414509_North_Rhine_Westphalia_20200228_null_1",
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]
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"Global MG94xREV":0.008102221891915536,
"Nucleotide GTR":0.007761298330307575,
"amino-acid": [
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"epi_isl_417453_Washington_20200314_null_1":{
"Global MG94xREV":0.008161046899054218,
"Nucleotide GTR":0.007817648111364714,
"amino-acid": [
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"original name":"epi_isl_417453_Washington_20200314_null_1",
"synonymous substitution count": [
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"epi_isl_417456_Washington_20200313_null_1":{
"Global MG94xREV":0.008148900176563547,
"Nucleotide GTR":0.007806012496067671,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_417456_Washington_20200313_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417576_Reykjavik_20200317_null_2":{
"Global MG94xREV":0.008151830012186253,
"Nucleotide GTR":0.00780881905069305,
"amino-acid": [
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"codon": [
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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":0.008163058641472928,
"Nucleotide GTR":0.007819575204115768,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_418004_Portugal_20200312_null_1",
"synonymous substitution count": [
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"epi_isl_418052_Washington_20200316_null_1":{
"Global MG94xREV":0.3767867175337203,
"Nucleotide GTR":0.3609323665394153,
"amino-acid": [
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"codon": [
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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":{
"Global MG94xREV":2.07143000830514,
"Nucleotide GTR":1.984268819007466,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_418065_Washington_20200313_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418078_Washington_20200315_null_1":{
"Global MG94xREV":0.4061146575875261,
"Nucleotide GTR":0.3890262517979875,
"amino-acid": [
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"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":0.008102483859287917,
"Nucleotide GTR":0.007761549274672823,
"amino-acid": [
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"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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]
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"epi_isl_418991_Hangzhou_20200204_null_1":{
"Global MG94xREV":0.001515355080412991,
"Nucleotide GTR":0.001451592293117494,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418991_Hangzhou_20200204_null_1",
"synonymous substitution count": [
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]
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"epi_isl_419431_Wales_20200317_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_419431_Wales_20200317_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_419575_Luxembourg_20200314_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_419575_Luxembourg_20200314_null_1",
"synonymous substitution count": [
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"epi_isl_420084_Taiwan_20200321_null_2":{
"Global MG94xREV":0.008155611369844745,
"Nucleotide GTR":0.007812441297191925,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_420084_Taiwan_20200321_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_420106_Singapore_20200306_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "ILVF", "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": [
[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, 0, 0, 0, 0]
],
"original name":"epi_isl_420106_Singapore_20200306_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_420107_Singapore_20200309_null_14":{
"Global MG94xREV":0.009619538745895219,
"Nucleotide GTR":0.009214769849902776,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_420107_Singapore_20200309_null_14",
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_420388_Vilvoorde_20200324_null_1":{
"Global MG94xREV":0.008155095791954598,
"Nucleotide GTR":0.007811947413678085,
"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, 1, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_420388_Vilvoorde_20200324_null_1",
"synonymous substitution count": [
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]
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"epi_isl_421952_England_20200331_null_1":{
"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, 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]
],
"original name":"epi_isl_421952_England_20200331_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_421996_England_20200401_null_1":{
"Global MG94xREV":0.008158255244661202,
"Nucleotide GTR":0.007814973923608763,
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_421996_England_20200401_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_422349_Wales_20200324_null_2":{
"Global MG94xREV":0.008302196901806983,
"Nucleotide GTR":0.007952858834460435,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422349_Wales_20200324_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_422565_Pichincha_20200330_null_5669":{
"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_422565_Pichincha_20200330_null_5669",
"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_422580_Netherlands_20200330_null_1":{
"Global MG94xREV":0.008153631613853273,
"Nucleotide GTR":0.007810544844950059,
"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", "-"]
],
"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_422580_Netherlands_20200330_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, 1, 0, 0]
]
},
"epi_isl_422718_Netherlands_20200323_null_3":{
"Global MG94xREV":0.008156120306590887,
"Nucleotide GTR":0.007812928819006406,
"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", "-"]
],
"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_422718_Netherlands_20200323_null_3",
"synonymous substitution count": [
[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, 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":696.7374319348119,
"Equilibrium frequencies": [
[0.01437330308389393],
[0.01110869092302692],
[0.008340884881659653],
[0.02203786033811293],
[0.006324818316895896],
[0.004888260646602973],
[0.003670317196452597],
[0.009697524773402936],
[0.004050041933688656],
[0.003130154829689778],
[0.002350255424074701],
[0.006209724930809095],
[0.03110558030544641],
[0.02404056155900562],
[0.01805069182710506],
[0.0476926166870804],
[0.01517862838126288],
[0.01173110247093278],
[0.008808218351108971],
[0.02327262497965544],
[0.006679193102018626],
[0.005162146192316796],
[0.003875962292114963],
[0.01024086974959248],
[0.004276962719089705],
[0.003305535036613506],
[0.002481938457350945],
[0.006557651120585678],
[0.03284840243638633],
[0.02538753603476946],
[0.01906205843355114],
[0.05036479791721564],
[0.01202086239564659],
[0.009290560715379979],
[0.006975754204523219],
[0.01843098173556109],
[0.005289651948553572],
[0.004088211891441554],
[0.00306960604040774],
[0.008110356415574126],
[0.003387182229255566],
[0.002617850626619895],
[0.00196559530419156],
[0.00519339559406615],
[0.02601461184016212],
[0.0201059061183163],
[0.01509638260136571],
[0.03988689163078545],
[0.02172338552415813],
[0.04309571123812793],
[0.01236837604180533],
[0.009559143494451651],
[0.007177417753986941],
[0.01896380687359193],
[0.006121113692586963],
[0.00459599650500554],
[0.01214330739829292],
[0.06082791551317655],
[0.04701205484806426],
[0.03529868102866681],
[0.09326437346472154]
],
"Log Likelihood":-301.4834700657666,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.4795994975586605, 1]
]
},
"display order":1,
"estimated parameters":45
},
"Nucleotide GTR":{
"AIC-c":735.1555256837465,
"Equilibrium frequencies": [
[0.2261246312684366],
[0.1859328908554572],
[0.1302544247787611],
[0.4576880530973451]
],
"Log Likelihood":-309.5979169616124,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.1191802403706874,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.06467947131928599,
"Substitution rate from nucleotide C to nucleotide G":0.1104521343100991,
"Substitution rate from nucleotide C to nucleotide T":0.8795030029129813,
"Substitution rate from nucleotide G to nucleotide T":0.4231082715729154
},
"display order":0,
"estimated parameters":57
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-11/sequences.ORF7b.compressed.fas",
"number of sequences":26,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_419575_Luxembourg_20200314_null_1,epi_isl_421952_England_20200331_null_1,epi_isl_420106_Singapore_20200306_null_1,epi_isl_422565_Pichincha_20200330_null_5669,epi_isl_417456_Washington_20200313_null_1,epi_isl_417253_England_20200303_null_1,epi_isl_418004_Portugal_20200312_null_1,epi_isl_418638_Li_ge_20200319_null_1,epi_isl_422718_Netherlands_20200323_null_3,((epi_isl_418991_Hangzhou_20200204_null_1,epi_isl_418052_Washington_20200316_null_1)Node31,epi_isl_413752_China_20200201_null_1,epi_isl_413747_China_20200201_null_1,epi_isl_418065_Washington_20200313_null_1)Node30,epi_isl_422349_Wales_20200324_null_2,epi_isl_419431_Wales_20200317_null_1,epi_isl_421996_England_20200401_null_1,epi_isl_417576_Reykjavik_20200317_null_2,epi_isl_417453_Washington_20200314_null_1,epi_isl_414509_North_Rhine_Westphalia_20200228_null_1,epi_isl_420388_Vilvoorde_20200324_null_1,epi_isl_420084_Taiwan_20200321_null_2,((epi_isl_418078_Washington_20200315_null_1,epi_isl_420107_Singapore_20200309_null_14)Node10,epi_isl_413875_Guangdong_20200210_null_1)Node9,epi_isl_422580_Netherlands_20200330_null_1)"
}
},
"tested":{
"0":{
"Node10":"test",
"Node30":"test",
"Node31":"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_417253_England_20200303_null_1":"test",
"epi_isl_417453_Washington_20200314_null_1":"test",
"epi_isl_417456_Washington_20200313_null_1":"test",
"epi_isl_417576_Reykjavik_20200317_null_2":"test",
"epi_isl_418004_Portugal_20200312_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_418991_Hangzhou_20200204_null_1":"test",
"epi_isl_419431_Wales_20200317_null_1":"test",
"epi_isl_419575_Luxembourg_20200314_null_1":"test",
"epi_isl_420084_Taiwan_20200321_null_2":"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_421952_England_20200331_null_1":"test",
"epi_isl_421996_England_20200401_null_1":"test",
"epi_isl_422349_Wales_20200324_null_2":"test",
"epi_isl_422565_Pichincha_20200330_null_5669":"test",
"epi_isl_422580_Netherlands_20200330_null_1":"test",
"epi_isl_422718_Netherlands_20200323_null_3":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}