{
"MLE":{
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"NAMES": [
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["Node95"],
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["epi_isl_419431_Wales_20200317_null_1"],
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["epi_isl_422580_Netherlands_20200330_null_1"],
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["epi_isl_425436_England_20200401_null_1"],
["epi_isl_426093_Washington_20200325_null_5"],
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["epi_isl_423040_Bangkok_20200320_null_3"],
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["Node86"],
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["epi_isl_419575_Luxembourg_20200314_null_1"],
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["Node24"],
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["epi_isl_418004_Portugal_20200312_null_1"],
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["epi_isl_418991_Hangzhou_20200204_null_1"],
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["Node16"],
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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":{
"Node16":{
"Global MG94xREV":0.02456671359913259,
"Nucleotide GTR":0.0235469552535486,
"amino-acid": [
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"Global MG94xREV":0.008101287017973529,
"Nucleotide GTR":0.007765004551325601,
"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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"Global MG94xREV":0.008143302368356396,
"Nucleotide GTR":0.007805275854666004,
"amino-acid": [
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"Global MG94xREV":0.008146000259604122,
"Nucleotide GTR":0.007807861757099912,
"amino-acid": [
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"original name":"epi_isl_418004_Portugal_20200312_null_1",
"synonymous substitution count": [
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"epi_isl_418035_Connecticut_20200314_null_1":{
"Global MG94xREV":0.5698393561147393,
"Nucleotide GTR":0.5461854621294761,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_418035_Connecticut_20200314_null_1",
"synonymous substitution count": [
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"Global MG94xREV":0.02542209611557616,
"Nucleotide GTR":0.02436683104841584,
"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":0.2820950106178168,
"Nucleotide GTR":0.2703853148880925,
"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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"epi_isl_418078_Washington_20200315_null_1":{
"Global MG94xREV":0.3315288778942413,
"Nucleotide GTR":0.3177671942782983,
"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":0.008103554478273156,
"Nucleotide GTR":0.007767177889896058,
"amino-acid": [
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"codon": [
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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,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_418991_Hangzhou_20200204_null_1",
"synonymous substitution count": [
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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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"original name":"epi_isl_419431_Wales_20200317_null_1",
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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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"original name":"epi_isl_419575_Luxembourg_20200314_null_1",
"synonymous substitution count": [
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"epi_isl_420106_Singapore_20200306_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"synonymous substitution count": [
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"epi_isl_420107_Singapore_20200309_null_14":{
"Global MG94xREV":0.005609251260079068,
"Nucleotide GTR":0.005376412595604832,
"amino-acid": [
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"codon": [
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"epi_isl_420388_Vilvoorde_20200324_null_1":{
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"Nucleotide GTR":0.0006587209463419356,
"amino-acid": [
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"original name":"epi_isl_420388_Vilvoorde_20200324_null_1",
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]
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"epi_isl_421952_England_20200331_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", "LF", "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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"original name":"epi_isl_421952_England_20200331_null_1",
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"epi_isl_421996_England_20200401_null_1":{
"Global MG94xREV":0.0001502158612533488,
"Nucleotide GTR":0.0001439804371485308,
"amino-acid": [
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"original name":"epi_isl_421996_England_20200401_null_1",
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]
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"epi_isl_422349_Wales_20200324_null_2":{
"Global MG94xREV":0.005640192078721165,
"Nucleotide GTR":0.005406069068341146,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422349_Wales_20200324_null_2",
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]
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"epi_isl_422580_Netherlands_20200330_null_1":{
"Global MG94xREV":0.008140401178625946,
"Nucleotide GTR":0.007802495092620258,
"amino-acid": [
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"original name":"epi_isl_422580_Netherlands_20200330_null_1",
"synonymous substitution count": [
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"epi_isl_422998_Washington_20200317_null_1":{
"Global MG94xREV":0.3257023414311259,
"Nucleotide GTR":0.3121825159359339,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422998_Washington_20200317_null_1",
"synonymous substitution count": [
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"epi_isl_423009_Washington_20200318_null_1":{
"Global MG94xREV":0.008237128551890403,
"Nucleotide GTR":0.007895207335992201,
"amino-acid": [
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"codon": [
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"synonymous substitution count": [
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"epi_isl_423024_Washington_20200317_null_1":{
"Global MG94xREV":0.3347677489009706,
"Nucleotide GTR":0.3208716205321286,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_423024_Washington_20200317_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423040_Bangkok_20200320_null_3":{
"Global MG94xREV":0.008143390223281368,
"Nucleotide GTR":0.007805360062754261,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_423040_Bangkok_20200320_null_3",
"synonymous substitution count": [
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"epi_isl_423058_England_20200324_null_1":{
"Global MG94xREV":0.008102346174451786,
"Nucleotide GTR":0.007766019742474356,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_423058_England_20200324_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423141_England_20200323_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_423141_England_20200323_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423152_England_20200324_null_1":{
"Global MG94xREV":0.004003724748771575,
"Nucleotide GTR":0.003837531101847426,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_423152_England_20200324_null_1",
"synonymous substitution count": [
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"epi_isl_423277_England_20200306_null_1":{
"Global MG94xREV":0.008142095603815173,
"Nucleotide GTR":0.007804119182629292,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_423277_England_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423428_England_20200330_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_423428_England_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423468_England_20200330_null_2":{
"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", "-"]
],
"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_423468_England_20200330_null_2",
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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]
]
},
"epi_isl_423531_England_20200326_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", "HY", "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, 1, 0, 0]
],
"original name":"epi_isl_423531_England_20200326_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_423567_England_20200401_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["MI", "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": [
[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, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423567_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_423669_England_20200320_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "YF", "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, 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]
],
"original name":"epi_isl_423669_England_20200320_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_423823_England_20200322_null_1":{
"Global MG94xREV":0.008102784258602096,
"Nucleotide GTR":0.00776643964185743,
"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", "C", "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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423823_England_20200322_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_423826_England_20200322_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "SL", "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, 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, 0, 0, 0]
],
"original name":"epi_isl_423826_England_20200322_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_423881_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["ML", "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": [
[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, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423881_England_20200318_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423896_England_20200318_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", "-"]
],
"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_423896_England_20200318_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424002_England_20200320_null_2":{
"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", "-"]
],
"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_424002_England_20200320_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_424220_Washington_20200321_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "P", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424220_Washington_20200321_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_424341_Washington_20200324_null_3":{
"Global MG94xREV":0.003983443744060636,
"Nucleotide GTR":0.003818091956741652,
"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": [
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],
"original name":"epi_isl_424341_Washington_20200324_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_424374_Reykjavik_20200301_null_1":{
"Global MG94xREV":0.008197232377151214,
"Nucleotide GTR":0.007856967241826548,
"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", "G", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424374_Reykjavik_20200301_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424396_Reykjavik_20200319_null_3":{
"Global MG94xREV":0.008141936018463502,
"Nucleotide GTR":0.007803966221627022,
"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": [
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],
"original name":"epi_isl_424396_Reykjavik_20200319_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_424964_New_York_20200401_null_3":{
"Global MG94xREV":0.008143151163761405,
"Nucleotide GTR":0.00780513092653722,
"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": [
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],
"original name":"epi_isl_424964_New_York_20200401_null_3",
"synonymous substitution count": [
[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, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_425245_England_20200331_null_1":{
"Global MG94xREV":0.008190653511339579,
"Nucleotide GTR":0.00785066146314514,
"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", "DAGV", "H", "N", "E", "T", "C", "Y", "A", "-"]
],
"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", "GNT", "CAT", "AAT", "GAA", "ACT", "TGT", "TAC", "GCC", "---"]
],
"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, 3, 0, 0, 0, 0, 0, 1, 0, 0]
],
"original name":"epi_isl_425245_England_20200331_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_425436_England_20200401_null_1":{
"Global MG94xREV":0.008185854210358222,
"Nucleotide GTR":0.00784606137998789,
"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": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTT", "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", "---"]
],
"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_425436_England_20200401_null_1",
"synonymous substitution count": [
[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, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_425725_Scotland_20200318_null_2":{
"Global MG94xREV":0.004001236241437714,
"Nucleotide GTR":0.003835145891851709,
"amino-acid": [
["M", "I", "E", "L", "L", "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": [
["ATG", "ATT", "GAA", "CTT", "TTA", "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", "---"]
],
"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_425725_Scotland_20200318_null_2",
"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_425745_Scotland_20200319_null_1":{
"Global MG94xREV":0.00810757179814472,
"Nucleotide GTR":0.00777102845179043,
"amino-acid": [
["M", "V", "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": [
["ATG", "GTT", "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", "---"]
],
"nonsynonymous substitution count": [
[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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_425745_Scotland_20200319_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_426093_Washington_20200325_null_5":{
"Global MG94xREV":0.008142554784167968,
"Nucleotide GTR":0.007804559302516596,
"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": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "TTG", "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", "---"]
],
"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_426093_Washington_20200325_null_5",
"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]
]
},
"epi_isl_426457_Virginia_20200330_null_8594":{
"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", "-"]
],
"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", "---"]
],
"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_426457_Virginia_20200330_null_8594",
"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":951.5229568884573,
"Equilibrium frequencies": [
[0.0142586551448434],
[0.01113500816214584],
[0.00823680582504643],
[0.02215713244908055],
[0.006109497234899793],
[0.004771088218780524],
[0.003529276912958145],
[0.009493808361016565],
[0.004025404916446937],
[0.003143558501503469],
[0.002325358059869455],
[0.006255248407992436],
[0.03022673282159174],
[0.02360495525450357],
[0.01746109478403711],
[0.04697060948789319],
[0.01533024724179957],
[0.01197184632289014],
[0.008855833071067902],
[0.02382232511854718],
[0.006568649159593187],
[0.005129653621842038],
[0.003794515479251934],
[0.01020730412245666],
[0.004327929386791046],
[0.003379808863989356],
[0.002500117551156444],
[0.006725354086993061],
[0.03249838661217643],
[0.02537895730748667],
[0.01877336238464204],
[0.05050062921311559],
[0.01233795533231084],
[0.009635076515554574],
[0.007127274018341984],
[0.01917247508070323],
[0.005286522692452573],
[0.0041284029055936],
[0.003053868717989233],
[0.008214953114572156],
[0.003483166227745404],
[0.002720108171637935],
[0.002012122713036794],
[0.005412640579797599],
[0.02615506691241945],
[0.02042527016698249],
[0.01510901310889806],
[0.04064347414998842],
[0.02210623139182966],
[0.043988355443145],
[0.01212912982152777],
[0.009471998459215251],
[0.007006641660930751],
[0.01884797221180254],
[0.006240878373509612],
[0.004616512407694901],
[0.01241848831243306],
[0.06000886036569816],
[0.04686270501568105],
[0.03466535417215248],
[0.09325032786994707]
],
"Log Likelihood":-397.0050017602908,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.6352210435977816, 1]
]
},
"display order":1,
"estimated parameters":76
},
"Nucleotide GTR":{
"AIC-c":1022.840732457135,
"Equilibrium frequencies": [
[0.2255649458019474],
[0.185880948006614],
[0.1311317288260151],
[0.4574223773654235]
],
"Log Likelihood":-404.706476484188,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.3214037053835967,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.179165672175653,
"Substitution rate from nucleotide C to nucleotide G":0,
"Substitution rate from nucleotide C to nucleotide T":0.9176499095747541,
"Substitution rate from nucleotide G to nucleotide T":0.5615144680960106
},
"display order":0,
"estimated parameters":105
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-17/sequences.ORF7b.compressed.fas",
"number of sequences":50,
"number of sites":44,
"partition count":1,
"trees":{
"0":"((epi_isl_423896_England_20200318_null_1,epi_isl_424341_Washington_20200324_null_3)Node95,epi_isl_420106_Singapore_20200306_null_1,epi_isl_423881_England_20200318_null_1,epi_isl_423669_England_20200320_null_1,epi_isl_423567_England_20200401_null_1,epi_isl_423141_England_20200323_null_1,epi_isl_421952_England_20200331_null_1,epi_isl_419431_Wales_20200317_null_1,epi_isl_426457_Virginia_20200330_null_8594,epi_isl_422580_Netherlands_20200330_null_1,epi_isl_423058_England_20200324_null_1,epi_isl_425436_England_20200401_null_1,epi_isl_426093_Washington_20200325_null_5,(epi_isl_421996_England_20200401_null_1,epi_isl_422998_Washington_20200317_null_1)Node64,epi_isl_424374_Reykjavik_20200301_null_1,epi_isl_423277_England_20200306_null_1,epi_isl_423040_Bangkok_20200320_null_3,epi_isl_414509_North_Rhine_Westphalia_20200228_null_1,epi_isl_423428_England_20200330_null_1,((epi_isl_418078_Washington_20200315_null_1,epi_isl_420107_Singapore_20200309_null_14)Node86,epi_isl_420388_Vilvoorde_20200324_null_1)Node85,epi_isl_423468_England_20200330_null_2,(epi_isl_419575_Luxembourg_20200314_null_1,epi_isl_423152_England_20200324_null_1)Node24,epi_isl_424964_New_York_20200401_null_3,epi_isl_417253_England_20200303_null_1,epi_isl_418004_Portugal_20200312_null_1,epi_isl_423531_England_20200326_null_1,(epi_isl_418991_Hangzhou_20200204_null_1,epi_isl_423024_Washington_20200317_null_1)Node16,epi_isl_425245_England_20200331_null_1,(epi_isl_423826_England_20200322_null_2,epi_isl_425725_Scotland_20200318_null_2)Node55,epi_isl_425745_Scotland_20200319_null_1,(epi_isl_422349_Wales_20200324_null_2,epi_isl_423009_Washington_20200318_null_1)Node32,epi_isl_413875_Guangdong_20200210_null_1,((epi_isl_418052_Washington_20200316_null_1,epi_isl_418035_Connecticut_20200314_null_1)Node38,epi_isl_424002_England_20200320_null_2)Node37,(epi_isl_424220_Washington_20200321_null_2,epi_isl_413747_China_20200201_null_1,epi_isl_418065_Washington_20200313_null_1)Node42,epi_isl_418638_Li_ge_20200319_null_1,epi_isl_423823_England_20200322_null_1,epi_isl_417453_Washington_20200314_null_1,epi_isl_424396_Reykjavik_20200319_null_3)"
}
},
"tested":{
"0":{
"Node16":"test",
"Node24":"test",
"Node32":"test",
"Node37":"test",
"Node38":"test",
"Node42":"test",
"Node55":"test",
"Node64":"test",
"Node85":"test",
"Node86":"test",
"Node95":"test",
"epi_isl_413747_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_418004_Portugal_20200312_null_1":"test",
"epi_isl_418035_Connecticut_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_418991_Hangzhou_20200204_null_1":"test",
"epi_isl_419431_Wales_20200317_null_1":"test",
"epi_isl_419575_Luxembourg_20200314_null_1":"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_422580_Netherlands_20200330_null_1":"test",
"epi_isl_422998_Washington_20200317_null_1":"test",
"epi_isl_423009_Washington_20200318_null_1":"test",
"epi_isl_423024_Washington_20200317_null_1":"test",
"epi_isl_423040_Bangkok_20200320_null_3":"test",
"epi_isl_423058_England_20200324_null_1":"test",
"epi_isl_423141_England_20200323_null_1":"test",
"epi_isl_423152_England_20200324_null_1":"test",
"epi_isl_423277_England_20200306_null_1":"test",
"epi_isl_423428_England_20200330_null_1":"test",
"epi_isl_423468_England_20200330_null_2":"test",
"epi_isl_423531_England_20200326_null_1":"test",
"epi_isl_423567_England_20200401_null_1":"test",
"epi_isl_423669_England_20200320_null_1":"test",
"epi_isl_423823_England_20200322_null_1":"test",
"epi_isl_423826_England_20200322_null_2":"test",
"epi_isl_423881_England_20200318_null_1":"test",
"epi_isl_423896_England_20200318_null_1":"test",
"epi_isl_424002_England_20200320_null_2":"test",
"epi_isl_424220_Washington_20200321_null_2":"test",
"epi_isl_424341_Washington_20200324_null_3":"test",
"epi_isl_424374_Reykjavik_20200301_null_1":"test",
"epi_isl_424396_Reykjavik_20200319_null_3":"test",
"epi_isl_424964_New_York_20200401_null_3":"test",
"epi_isl_425245_England_20200331_null_1":"test",
"epi_isl_425436_England_20200401_null_1":"test",
"epi_isl_425725_Scotland_20200318_null_2":"test",
"epi_isl_425745_Scotland_20200319_null_1":"test",
"epi_isl_426093_Washington_20200325_null_5":"test",
"epi_isl_426457_Virginia_20200330_null_8594":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":2
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":4
}
}
}