{
"MLE":{
"content":{
"0":{
"by-branch":{
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"NAMES": [
["epi_isl_421560_Utah_20200318_null_15"],
["epi_isl_418926_Washington_20200314_null_2"],
["epi_isl_419663_Austria_20200315_null_2"],
["epi_isl_417342_Washington_20200313_null_4863"],
["epi_isl_420901_Munich_20200312_null_5"],
["epi_isl_415654_Hauts_de_France_20200309_null_1"],
["epi_isl_416566_unknown_20200215_null_1"],
["epi_isl_415710_Saint_Petersburg_20200315_null_1"],
["epi_isl_416502_Bretagne_20200226_null_1"],
["epi_isl_421251_Jiangxi_20200203_null_5"],
["epi_isl_420323_Waterloo_20200307_null_2"],
["epi_isl_413221_Scotland_20200302_null_1"],
["epi_isl_419953_Victoria_20200321_null_2"],
["epi_isl_420589_New_York_20200318_null_1"],
["epi_isl_421317_Wisconsin_20200324_null_3"],
["epi_isl_415621_Washington_20200309_null_1"],
["epi_isl_417176_Hong_Kong_20200121_null_1"],
["epi_isl_418398_Finland_20200313_null_2"],
["epi_isl_419253_Hong_Kong_20200226_null_1"],
["epi_isl_421510_Hauts_de_France_20200323_null_3"],
["epi_isl_415527_Utrecht_20200312_null_1"],
["epi_isl_413890_Guangdong_20200228_null_1"],
["epi_isl_419885_Victoria_20200319_null_1"],
["epi_isl_420239_South_Yorkshire_20200323_null_1"],
["epi_isl_420352_Sint_Gillis_Waas_20200307_null_2"],
["epi_isl_416355_Shanghai_20200204_null_2"],
["epi_isl_418396_Finland_20200313_null_1"],
["epi_isl_419973_Victoria_20200322_null_4"],
["epi_isl_420664_England_20200326_null_1"]
],
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[1.614336910181007, 1.330306578548115, 0, 0, 0.5482283055181454, 0, 0, 0, 1, 1, 0.08173143151637255],
[0.8126538873562781, 2.187346112643722, 1, 0, 0.2708846291187594, 1.230536167436786, 0, -15.05584992953762, 1, 0.2708846291187594, 0.08173143151637255],
[0.8102520381059594, 2.18974796189404, 0, 0, 0.2700840127019865, 0, 0, 0, 1, 1, 0.08173143151637255],
[1.810252038105959, 1.189747961894041, 0, 0, 0.6034173460353198, 0, 0, 0, 1, 1, 0.08173143151637255],
[0.9446434887291224, 2.055356511270878, 0, 0, 0.3148811629097074, 0, 0, 0, 1, 1, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[0, 3, 0, 0, 0, null, 0, null, 1, 1, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[1, 2, 0, 1, 0.3333333333333333, 0, 0.5, 6.117597486345744, 0.6666666666666667, 1, 0.08173143151637255],
[0.9446434887291224, 2.055356511270878, 0, 0, 0.3148811629097074, 0, 0, 0, 1, 1, 0.08173143151637255],
[1.603385097800064, 1.338862588351619, 0, 1, 0.5449524543248817, 0, 0.746902638627897, 9.138499409230052, 0.4550475456751183, 1, 0.08173143151637255],
[1, 2, 1, 1, 0.3333333333333333, 1, 0.5, -6.117597486345744, 0.8888888888888891, 0.5555555555555555, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.08173143151637255],
[1.806750699439219, 1.192259984955491, 1, 0, 0.6024489038470616, 0.5534797912685911, 0, -6.7719331596158, 1, 0.6024489038470616, 0.08173143151637255],
[0.6696934214518848, 1.520054540442156, 0, 0, 0.3058312797207163, 0, 0, 0, 1, 1, 0.08173143151637255]
]
}
}
},
"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":{
"Node29":{
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
"codon": [
["AAT", "AAT", "GAG", "CTT", "AGT", "CCT", "GTT", "GCA", "CTA", "CGA", "CAG", "ATG", "TCT", "TGT", "GCT", "GCC", "GGT", "ACT", "ACA", "CAA", "ACT", "GCT", "TGC", "ACT", "GAT", "GAC", "AAT", "GCG", "TTA", "GCT", "TAC", "TAC", "AAC", "ACA", "ACA", "AAG", "GGA", "GGT", "AGG", "TTT", "GTA", "CTT", "GCA", "CTG", "TTA", "TCC", "GAT", "TTA", "CAG", "GAT", "TTG", "AAA", "TGG", "GCT", "AGA", "TTC", "CCT", "AAG", "AGT", "GAT", "GGA", "ACT", "GGT", "ACT", "ATC", "TAT", "ACA", "GAA", "CTG", "GAA", "CCA", "CCT", "TGT", "AGG", "TTT", "GTT", "ACA", "GAC", "ACA", "CCT", "AAA", "GGT", "CCT", "AAA", "GTG", "AAG", "TAT", "TTA", "TAC", "TTT", "ATT", "AAA", "GGA", "TTA", "AAC", "AAC", "CTA", "AAT", "AGA", "GGT", "ATG", "GTA", "CTT", "GGT", "AGT", "TTA", "GCT", "GCC", "ACA", "GTA", "CGT", "CTA", "CAA"]
],
"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]
],
"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]
]
},
"epi_isl_413221_Scotland_20200302_null_1":{
"Global MG94xREV":0.002921373549652504,
"Nucleotide GTR":0.002960315056012195,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
"codon": [
["AAT", "AAT", "GAG", "CTT", "AGT", "CCT", "GTT", "GCA", "CTA", "CGA", "CAG", "ATG", "TCT", "TGT", "GCT", "GCT", "GGT", "ACT", "ACA", "CAA", "ACT", "GCT", "TGC", "ACT", "GAT", "GAC", "AAT", "GCG", "TTA", "GCT", "TAC", "TAC", "AAC", "ACA", "ACA", "AAG", "GGA", "GGT", "AGG", "TTT", "GTA", "CTT", "GCA", "CTG", "TTA", "TCC", "GAT", "TTA", "CAG", "GAT", "TTG", "AAA", "TGG", "GCT", "AGA", "TTC", "CCT", "AAG", "AGT", "GAT", "GGA", "ACT", "GGT", "ACT", "ATC", "TAT", "ACA", "GAA", "CTG", "GAA", "CCA", "CCT", "TGT", "AGG", "TTT", "GTT", "ACA", "GAC", "ACA", "CCT", "AAA", "GGT", "CCT", "AAA", "GTG", "AAG", "TAT", "TTA", "TAC", "TTT", "ATT", "AAA", "GGA", "TTA", "AAC", "AAC", "CTA", "AAT", "AGA", "GGT", "ATG", "GTA", "CTT", "GGT", "AGT", "TTA", "GCT", "GCC", "ACA", "GTA", "CGT", "CTA", "CAA"]
],
"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]
],
"original name":"epi_isl_413221_Scotland_20200302_null_1",
"synonymous substitution count": [
[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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_413890_Guangdong_20200228_null_1":{
"Global MG94xREV":0.00291716220492633,
"Nucleotide GTR":0.002956047574641856,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_413890_Guangdong_20200228_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, 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, 0, 0, 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_415527_Utrecht_20200312_null_1":{
"Global MG94xREV":0.002917138444239845,
"Nucleotide GTR":0.0029560234972287,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_415527_Utrecht_20200312_null_1",
"synonymous substitution count": [
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]
},
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"Global MG94xREV":0.002921361117315357,
"Nucleotide GTR":0.002960302457953712,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "I", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
"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, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_415621_Washington_20200309_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.002917138432632324,
"Nucleotide GTR":0.002956023485466449,
"amino-acid": [
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]
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"Global MG94xREV":0.002921220706331988,
"Nucleotide GTR":0.002960160175311304,
"amino-acid": [
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],
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"original name":"epi_isl_415710_Saint_Petersburg_20200315_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.002921361090693884,
"Nucleotide GTR":0.002960302430977376,
"amino-acid": [
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],
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],
"original name":"epi_isl_416355_Shanghai_20200204_null_2",
"synonymous substitution count": [
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]
},
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"Global MG94xREV":0.002918595330944497,
"Nucleotide GTR":0.002957499804032117,
"amino-acid": [
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],
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],
"original name":"epi_isl_416502_Bretagne_20200226_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_416566_unknown_20200215_null_1":{
"Global MG94xREV":0.002917173693078118,
"Nucleotide GTR":0.002956059215929119,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416566_unknown_20200215_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_417176_Hong_Kong_20200121_null_1":{
"Global MG94xREV":0.002914095589265273,
"Nucleotide GTR":0.002952940081417129,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417176_Hong_Kong_20200121_null_1",
"synonymous substitution count": [
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.002960315060876791,
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"Nucleotide GTR":0.002963857943191036,
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"Global MG94xREV":0.002921367468489918,
"Nucleotide GTR":0.00296030889378855,
"amino-acid": [
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],
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"synonymous substitution count": [
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]
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"Global MG94xREV":0.002921405629563658,
"Nucleotide GTR":0.00296034756354414,
"amino-acid": [
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],
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"original name":"epi_isl_419253_Hong_Kong_20200226_null_1",
"synonymous substitution count": [
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]
},
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"Global MG94xREV":0.002918579819213391,
"Nucleotide GTR":0.002957484085531774,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
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],
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"Nucleotide GTR":0.002960352295261399,
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"original name":"epi_isl_419885_Victoria_20200319_null_1",
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"Nucleotide GTR":0.002960356721902345,
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"original name":"epi_isl_419953_Victoria_20200321_null_2",
"synonymous substitution count": [
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"Global MG94xREV":0.00292141466019623,
"Nucleotide GTR":0.002960356714553796,
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"original name":"epi_isl_419973_Victoria_20200322_null_4",
"synonymous substitution count": [
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"Global MG94xREV":0.00291131086727833,
"Nucleotide GTR":0.002950118239470306,
"amino-acid": [
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],
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"original name":"epi_isl_420239_South_Yorkshire_20200323_null_1",
"synonymous substitution count": [
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]
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"epi_isl_420323_Waterloo_20200307_null_2":{
"Global MG94xREV":0.002921361116379642,
"Nucleotide GTR":0.002960302457005517,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_420323_Waterloo_20200307_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_420352_Sint_Gillis_Waas_20200307_null_2":{
"Global MG94xREV":0.002914059984868755,
"Nucleotide GTR":0.002952904002418919,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "S", "A", "A", "T", "V", "R", "L", "Q"]
],
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_420352_Sint_Gillis_Waas_20200307_null_2",
"synonymous substitution count": [
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"Nucleotide GTR":0.00296168080348608,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "N", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
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"Global MG94xREV":0.002911318736048751,
"Nucleotide GTR":0.002950126213130347,
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"original name":"epi_isl_420664_England_20200326_null_1",
"synonymous substitution count": [
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"Nucleotide GTR":0.002960302431109227,
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"original name":"epi_isl_420901_Munich_20200312_null_5",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.002921361116379642,
"Nucleotide GTR":0.002960302457005517,
"amino-acid": [
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],
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"original name":"epi_isl_421251_Jiangxi_20200203_null_5",
"synonymous substitution count": [
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]
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"epi_isl_421317_Wisconsin_20200324_null_3":{
"Global MG94xREV":0.002921361147424528,
"Nucleotide GTR":0.002960302488464228,
"amino-acid": [
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],
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],
"original name":"epi_isl_421317_Wisconsin_20200324_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_421510_Hauts_de_France_20200323_null_3":{
"Global MG94xREV":0.002914060015139342,
"Nucleotide GTR":0.002952904033093012,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "P", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421510_Hauts_de_France_20200323_null_3",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_421560_Utah_20200318_null_15":{
"Global MG94xREV":0.002914060021293925,
"Nucleotide GTR":0.002952904039329632,
"amino-acid": [
["N", "N", "E", "L", "S", "P", "V", "A", "L", "R", "Q", "M", "S", "C", "A", "A", "G", "T", "T", "Q", "T", "A", "C", "T", "D", "D", "N", "A", "L", "A", "Y", "Y", "N", "T", "T", "K", "G", "G", "R", "F", "V", "L", "A", "L", "L", "S", "D", "L", "Q", "D", "L", "K", "W", "A", "R", "F", "P", "K", "S", "D", "G", "T", "G", "T", "I", "Y", "T", "E", "L", "E", "P", "P", "C", "R", "F", "V", "T", "D", "T", "P", "K", "G", "P", "K", "V", "K", "Y", "L", "Y", "F", "I", "K", "G", "L", "N", "N", "L", "N", "R", "G", "M", "V", "L", "G", "S", "L", "A", "A", "T", "V", "R", "L", "Q"]
],
"codon": [
["AAT", "AAT", "GAG", "CTT", "AGT", "CCT", "GTT", "GCA", "CTA", "CGA", "CAG", "ATG", "TCT", "TGT", "GCT", "GCC", "GGT", "ACT", "ACA", "CAA", "ACT", "GCT", "TGC", "ACT", "GAT", "GAC", "AAT", "GCG", "TTA", "GCT", "TAC", "TAC", "AAC", "ACA", "ACA", "AAG", "GGA", "GGT", "AGG", "TTT", "GTA", "CTT", "GCA", "CTG", "TTA", "TCC", "GAT", "TTA", "CAG", "GAT", "TTG", "AAA", "TGG", "GCT", "AGA", "TTC", "CCT", "AAG", "AGT", "GAT", "GGA", "ACT", "GGT", "ACT", "ATC", "TAT", "ACA", "GAA", "CTG", "GAA", "CCA", "CCT", "TGT", "AGG", "TTT", "GTT", "ACA", "GAC", "ACA", "CCT", "AAA", "GGT", "CCT", "AAA", "GTG", "AAG", "TAT", "TTA", "TAC", "TTT", "ATT", "AAA", "GGA", "TTA", "AAC", "AAC", "CTA", "AAT", "AGA", "GGT", "ATG", "GTA", "CTT", "GGT", "AGT", "TTA", "GCC", "GCC", "ACA", "GTA", "CGT", "CTA", "CAA"]
],
"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]
],
"original name":"epi_isl_421560_Utah_20200318_null_15",
"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, 1, 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, 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]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":1376.839048860964,
"Equilibrium frequencies": [
[0.03400782907267156],
[0.01163737107582153],
[0.01446540591455734],
[0.03938016916059899],
[0.02814826316913676],
[0.00963224623774526],
[0.01197300926387421],
[0.0325949463815799],
[0.02251716003138992],
[0.007705300632362783],
[0.009577790431758196],
[0.02607427745998002],
[0.02743380677853324],
[0.009387761530498051],
[0.01166911154443306],
[0.03176762472397821],
[0.0182957811588382],
[0.006260758192251701],
[0.007782205104035303],
[0.02118603205811009],
[0.01514340894396452],
[0.005182026434479067],
[0.006441327284857955],
[0.0175356681723819],
[0.01211394680244095],
[0.00414535411335777],
[0.005152729900817997],
[0.01402763091002404],
[0.01475904045804669],
[0.005050496759623343],
[0.006277834162210109],
[0.01709057960283215],
[0.0311446450240784],
[0.01065759858988454],
[0.01324753577699339],
[0.03606467754451889],
[0.02577840715953222],
[0.008821289039592442],
[0.01096497875817132],
[0.02985071562386051],
[0.0206213973444002],
[0.007056576663154042],
[0.008771417971864391],
[0.02387903426634731],
[0.02512410221630925],
[0.008597387966555441],
[0.01068666676785296],
[0.02909304775592117],
[0.008840668396195052],
[0.02991629420997435],
[0.02138364919240157],
[0.007317416824090722],
[0.009095645736209457],
[0.02476170180308212],
[0.005853556386565817],
[0.007276047882613951],
[0.01980808545093107],
[0.02084089155481184],
[0.007131686884688512],
[0.008864780969035271],
[0.02413320277317295]
],
"Log Likelihood":-643.8069006681056,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.4485617966659536, 1]
]
},
"display order":1,
"estimated parameters":44
},
"Nucleotide GTR":{
"AIC-c":1452.71361178321,
"Equilibrium frequencies": [
[0.309429356118401],
[0.1880785271081273],
[0.2123893805309734],
[0.2901027362424982]
],
"Log Likelihood":-662.9439872164746,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.556973809370616,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0,
"Substitution rate from nucleotide C to nucleotide G":0.270420765536271,
"Substitution rate from nucleotide C to nucleotide T":3.382210740882526,
"Substitution rate from nucleotide G to nucleotide T":0.1755124213049541
},
"display order":0,
"estimated parameters":63
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-09/sequences.nsp9.compressed.fas",
"number of sequences":29,
"number of sites":113,
"partition count":1,
"trees":{
"0":"(epi_isl_421560_Utah_20200318_null_15,epi_isl_418926_Washington_20200314_null_2,epi_isl_419663_Austria_20200315_null_2,epi_isl_417342_Washington_20200313_null_4863,epi_isl_420901_Munich_20200312_null_5,epi_isl_415654_Hauts_de_France_20200309_null_1,epi_isl_416566_unknown_20200215_null_1,epi_isl_415710_Saint_Petersburg_20200315_null_1,epi_isl_416502_Bretagne_20200226_null_1,epi_isl_421251_Jiangxi_20200203_null_5,epi_isl_420323_Waterloo_20200307_null_2,epi_isl_413221_Scotland_20200302_null_1,epi_isl_419953_Victoria_20200321_null_2,epi_isl_420589_New_York_20200318_null_1,epi_isl_421317_Wisconsin_20200324_null_3,epi_isl_415621_Washington_20200309_null_1,epi_isl_417176_Hong_Kong_20200121_null_1,epi_isl_418398_Finland_20200313_null_2,epi_isl_419253_Hong_Kong_20200226_null_1,epi_isl_421510_Hauts_de_France_20200323_null_3,epi_isl_415527_Utrecht_20200312_null_1,epi_isl_413890_Guangdong_20200228_null_1,epi_isl_419885_Victoria_20200319_null_1,epi_isl_420239_South_Yorkshire_20200323_null_1,epi_isl_420352_Sint_Gillis_Waas_20200307_null_2,epi_isl_416355_Shanghai_20200204_null_2,epi_isl_418396_Finland_20200313_null_1,epi_isl_419973_Victoria_20200322_null_4,epi_isl_420664_England_20200326_null_1)"
}
},
"tested":{
"0":{
"epi_isl_413221_Scotland_20200302_null_1":"test",
"epi_isl_413890_Guangdong_20200228_null_1":"test",
"epi_isl_415527_Utrecht_20200312_null_1":"test",
"epi_isl_415621_Washington_20200309_null_1":"test",
"epi_isl_415654_Hauts_de_France_20200309_null_1":"test",
"epi_isl_415710_Saint_Petersburg_20200315_null_1":"test",
"epi_isl_416355_Shanghai_20200204_null_2":"test",
"epi_isl_416502_Bretagne_20200226_null_1":"test",
"epi_isl_416566_unknown_20200215_null_1":"test",
"epi_isl_417176_Hong_Kong_20200121_null_1":"test",
"epi_isl_417342_Washington_20200313_null_4863":"test",
"epi_isl_418396_Finland_20200313_null_1":"test",
"epi_isl_418398_Finland_20200313_null_2":"test",
"epi_isl_418926_Washington_20200314_null_2":"test",
"epi_isl_419253_Hong_Kong_20200226_null_1":"test",
"epi_isl_419663_Austria_20200315_null_2":"test",
"epi_isl_419885_Victoria_20200319_null_1":"test",
"epi_isl_419953_Victoria_20200321_null_2":"test",
"epi_isl_419973_Victoria_20200322_null_4":"test",
"epi_isl_420239_South_Yorkshire_20200323_null_1":"test",
"epi_isl_420323_Waterloo_20200307_null_2":"test",
"epi_isl_420352_Sint_Gillis_Waas_20200307_null_2":"test",
"epi_isl_420589_New_York_20200318_null_1":"test",
"epi_isl_420664_England_20200326_null_1":"test",
"epi_isl_420901_Munich_20200312_null_5":"test",
"epi_isl_421251_Jiangxi_20200203_null_5":"test",
"epi_isl_421317_Wisconsin_20200324_null_3":"test",
"epi_isl_421510_Hauts_de_France_20200323_null_3":"test",
"epi_isl_421560_Utah_20200318_null_15":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":2
}
}
}