{
"MLE":{
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"NAMES": [
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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":{
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["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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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]
],
"synonymous substitution count": [
[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]
]
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"Node93":{
"Global MG94xREV":0.00556591009449638,
"Nucleotide GTR":0.005485621352508083,
"amino-acid": [
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"codon": [
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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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
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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]
]
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"Global MG94xREV":0.003131855235298501,
"Nucleotide GTR":0.003086677948446482,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "M", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
"original name":"epi_isl_407073_England_20200129_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414480_USA_20200221_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "IM", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_414480_USA_20200221_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414934_Shandong_20200121_null_1":{
"Global MG94xREV":0.008907155408323385,
"Nucleotide GTR":0.008778668909208774,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_414934_Shandong_20200121_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_414937_Shandong_20200126_null_1":{
"Global MG94xREV":0.01588730922454115,
"Nucleotide GTR":0.01565813339353395,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_414937_Shandong_20200126_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_415435_Wales_20200306_null_1":{
"Global MG94xREV":0.3940865662910804,
"Nucleotide GTR":0.3884018329581997,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_415435_Wales_20200306_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_416373_Shanghai_20200207_null_1":{
"Global MG94xREV":0.008943868456519427,
"Nucleotide GTR":0.008814852368459927,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "I", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416373_Shanghai_20200207_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_416567_unknown_20200215_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["R", "W", "A", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416567_unknown_20200215_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_416604_unknown_20200216_null_1":{
"Global MG94xREV":0.0110422386239233,
"Nucleotide GTR":0.01088295336189112,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "A", "F", "P", "F", "M", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416604_unknown_20200216_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_416677_Washington_20200312_null_1":{
"Global MG94xREV":0.00894519309275427,
"Nucleotide GTR":0.008816157896700741,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "V", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416677_Washington_20200312_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_417222_England_20200304_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "KN", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417222_England_20200304_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418113_Wales_20200313_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "D", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418113_Wales_20200313_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418182_Madrid_20200312_null_3":{
"Global MG94xREV":0.03398345777553217,
"Nucleotide GTR":0.03349324341222291,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "Q", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418182_Madrid_20200312_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_418999_Singapore_20200301_null_4":{
"Global MG94xREV":0.0004217150294183422,
"Nucleotide GTR":0.0004156317530781376,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "K", "KNTRSIM", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418999_Singapore_20200301_null_4",
"synonymous substitution count": [
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]
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"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
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"codon": [
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"synonymous substitution count": [
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]
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"Global MG94xREV":0.008894823572814891,
"Nucleotide GTR":0.008766514961510629,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_421291_Wisconsin_20200323_null_2",
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]
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"Global MG94xREV":0.00322354206639437,
"Nucleotide GTR":0.003177042188950589,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_421562_Utah_20200319_null_1",
"synonymous substitution count": [
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]
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"epi_isl_421881_England_20200326_null_4":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_421881_England_20200326_null_4",
"synonymous substitution count": [
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]
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"epi_isl_421889_England_20200327_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_421889_England_20200327_null_1",
"synonymous substitution count": [
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"epi_isl_422051_Wales_20200330_null_1":{
"Global MG94xREV":0.008942889690577164,
"Nucleotide GTR":0.008813887721302356,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422051_Wales_20200330_null_1",
"synonymous substitution count": [
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]
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"epi_isl_422206_Wales_20200330_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422206_Wales_20200330_null_1",
"synonymous substitution count": [
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]
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"epi_isl_422275_Wales_20200330_null_4":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422275_Wales_20200330_null_4",
"synonymous substitution count": [
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]
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"epi_isl_422359_Wales_20200324_null_1":{
"Global MG94xREV":0.008946660580939616,
"Nucleotide GTR":0.008817604216240112,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422359_Wales_20200324_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422425_Zhejiang_20200124_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_422425_Zhejiang_20200124_null_1",
"synonymous substitution count": [
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"epi_isl_422581_Netherlands_20200330_null_1":{
"Global MG94xREV":0.008946620564976001,
"Nucleotide GTR":0.008817564777510292,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422581_Netherlands_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_422636_Prague_20200308_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
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],
"original name":"epi_isl_422636_Prague_20200308_null_1",
"synonymous substitution count": [
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"epi_isl_422725_Netherlands_20200323_null_8":{
"Global MG94xREV":0.008890100568856531,
"Nucleotide GTR":0.008761860087299209,
"amino-acid": [
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"codon": [
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"synonymous substitution count": [
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]
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"epi_isl_422985_Washington_20200317_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_423043_Bangkok_20200318_null_2":{
"Global MG94xREV":0.008945397602248283,
"Nucleotide GTR":0.008816359456127337,
"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, 1, 0, 0]
],
"original name":"epi_isl_423043_Bangkok_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]
]
},
"epi_isl_423187_England_20200329_null_6":{
"Global MG94xREV":0.008942303278176744,
"Nucleotide GTR":0.008813309767952327,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "F", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "ACG", "---", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TTT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
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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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423187_England_20200329_null_6",
"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]
]
},
"epi_isl_423309_England_20200325_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "KQE", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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]
],
"original name":"epi_isl_423309_England_20200325_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]
]
},
"epi_isl_423534_England_20200331_null_3":{
"Global MG94xREV":0.003367576571920626,
"Nucleotide GTR":0.00331899898408353,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "L", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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]
],
"original name":"epi_isl_423534_England_20200331_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]
]
},
"epi_isl_423536_England_20200331_null_1":{
"Global MG94xREV":0.008889967311249657,
"Nucleotide GTR":0.008761728751945013,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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]
],
"original name":"epi_isl_423536_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, 1, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_423770_England_20200322_null_1":{
"Global MG94xREV":0.008892546252408932,
"Nucleotide GTR":0.008764270491651542,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "T", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423770_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]
]
},
"epi_isl_423807_England_20200324_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "Y"]
],
"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]
],
"original name":"epi_isl_423807_England_20200324_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, 1]
]
},
"epi_isl_423904_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "ILV", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423904_England_20200318_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_424158_England_20200321_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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]
],
"original name":"epi_isl_424158_England_20200321_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, 3, 0, 0]
]
},
"epi_isl_424288_Washington_20200322_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "V", "K", "L", "I", "L", "V", "V", "L", "S", "P", "C", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "GTA", "AAA", "TTA", "ATT", "TTA", "GTA", "GTG", "CTA", "TCC", "CCA", "TGT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"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]
],
"original name":"epi_isl_424288_Washington_20200322_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]
]
},
"epi_isl_424315_Idaho_20200320_null_1":{
"Global MG94xREV":0.3195284861312743,
"Nucleotide GTR":0.3149192596534205,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "EDAGV", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "AAG", "GNN", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"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, 13, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_424315_Idaho_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, 1, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_424366_Kayseri_20200317_null_3":{
"Global MG94xREV":0.008945149691451923,
"Nucleotide GTR":0.008816115121466005,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGT", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "ACG", "---", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"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]
],
"original name":"epi_isl_424366_Kayseri_20200317_null_3",
"synonymous 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]
]
},
"epi_isl_424479_Reykjavik_20200320_null_1":{
"Global MG94xREV":1.003124660129918,
"Nucleotide GTR":0.9886544987992653,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "Y", "G", "R", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TAT", "GGA", "AGA", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.5, 1.5, 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_424479_Reykjavik_20200320_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 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]
]
},
"epi_isl_424600_Reykjavik_20200327_null_1":{
"Global MG94xREV":0.008892007015207868,
"Nucleotide GTR":0.008763739032994476,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "R", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "ACG", "---", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CGA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"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]
],
"original name":"epi_isl_424600_Reykjavik_20200327_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]
]
},
"epi_isl_425131_Duesseldorf_20200320_null_1":{
"Global MG94xREV":0.008946520613078207,
"Nucleotide GTR":0.008817466267427396,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "Y", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_425131_Duesseldorf_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]
]
},
"epi_isl_425251_England_20200331_null_1":{
"Global MG94xREV":0.0002594312069108533,
"Nucleotide GTR":0.0002556888889643285,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "ACG", "---", "ATA", "TAT", "AGT", "CTA", "CTC", "CTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"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]
],
"original name":"epi_isl_425251_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]
]
},
"epi_isl_425750_Scotland_20200319_null_2":{
"Global MG94xREV":0.008946891284170156,
"Nucleotide GTR":0.0088178315915563,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "V", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_425750_Scotland_20200319_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]
]
},
"epi_isl_426014_Scotland_20200401_null_10":{
"Global MG94xREV":0.00894635006732473,
"Nucleotide GTR":0.00881729818181139,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "S", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "TCG", "TTT", "ACG", "---", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"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]
],
"original name":"epi_isl_426014_Scotland_20200401_null_10",
"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]
]
},
"epi_isl_426093_Washington_20200325_null_8":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "G", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TTA", "GGN", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"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]
],
"original name":"epi_isl_426093_Washington_20200325_null_8",
"synonymous substitution count": [
[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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_426103_Washington_20200323_null_2":{
"Global MG94xREV":0.9457779618944183,
"Nucleotide GTR":0.9321350317227932,
"amino-acid": [
["L", "G", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["TTA", "GGA", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[1.5, 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, 0, 0]
],
"original name":"epi_isl_426103_Washington_20200323_null_2",
"synonymous substitution count": [
[0.5, 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, 0, 0]
]
},
"epi_isl_426135_Washington_20200330_null_8379":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "ACG", "---", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"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]
],
"original name":"epi_isl_426135_Washington_20200330_null_8379",
"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]
]
},
"epi_isl_426167_South_Korea_20200223_null_4":{
"Global MG94xREV":0.003258836586722883,
"Nucleotide GTR":0.003211827582723313,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-"]
],
"codon": [
["ATG", "GGC", "TAT", "ATA", "AAC", "GTT", "TTC", "GCT", "TTT", "CCG", "TTT", "ACA", "---", "ATA", "TAT", "AGT", "CTA", "CTC", "TTG", "TGC", "AGA", "ATG", "AAT", "TCT", "CGT", "AAC", "TAC", "ATA", "GCA", "CAA", "GTA", "GAT", "GTA", "GTT", "AAC", "TTT", "AAT", "CTC", "ACA", "---"]
],
"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]
],
"original name":"epi_isl_426167_South_Korea_20200223_null_4",
"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]
]
}
},
"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]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":1175.099006760966,
"Equilibrium frequencies": [
[0.03133783582225225],
[0.02281262486945394],
[0.01455076124656537],
[0.03680248854114682],
[0.01601223163517058],
[0.01165623036918753],
[0.007434787803139469],
[0.01880442461355653],
[0.01536906607760041],
[0.01118803292642146],
[0.007136153636973712],
[0.01804910464836196],
[0.04649013633978647],
[0.03384286159595735],
[0.02158626645558474],
[0.05459702832147834],
[0.01342403172328427],
[0.009772129820192668],
[0.006233036693399541],
[0.01576489762963644],
[0.006859079441550838],
[0.004993121003549795],
[0.003184802801677905],
[0.008055157158339729],
[0.00658356983402347],
[0.004792561610741009],
[0.003056878380125506],
[0.00773160452913098],
[0.01991474678037455],
[0.01449709706336062],
[0.009246800810708007],
[0.02338745548166257],
[0.0177325891949779],
[0.01290857822995926],
[0.008233582980109061],
[0.02082477597861559],
[0.009060559487636708],
[0.006595705774680799],
[0.004206992423238408],
[0.01064052854866746],
[0.008696622721823019],
[0.00633077513423068],
[0.004038009567554357],
[0.01021312894361721],
[0.02630655460727658],
[0.01915006400784938],
[0.01221464039448482],
[0.03089385878408014],
[0.01986241460219905],
[0.03204305905085596],
[0.01394147255145825],
[0.01014880495411786],
[0.006473294444212005],
[0.01637256914395564],
[0.00974115647976973],
[0.006213280716869798],
[0.01571492985904804],
[0.04047786557565496],
[0.02946618165118827],
[0.01879465324608342],
[0.04753634528139086]
],
"Log Likelihood":-504.1008604853261,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.8156176159118439, 1]
]
},
"display order":1,
"estimated parameters":80
},
"Nucleotide GTR":{
"AIC-c":1230.047072535543,
"Equilibrium frequencies": [
[0.3008093525179856],
[0.1798561151079136],
[0.1584982014388489],
[0.3608363309352517]
],
"Log Likelihood":-510.1689656306525,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.4830067002119611,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.07943959838806097,
"Substitution rate from nucleotide C to nucleotide G":0.2021930285545476,
"Substitution rate from nucleotide C to nucleotide T":1.34569177107249,
"Substitution rate from nucleotide G to nucleotide T":0.6802529699775377
},
"display order":0,
"estimated parameters":103
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-15/sequences.ORF10.compressed.fas",
"number of sequences":49,
"number of sites":40,
"partition count":1,
"trees":{
"0":"((epi_isl_421562_Utah_20200319_null_1,epi_isl_424158_England_20200321_null_1)Node1,(epi_isl_418113_Wales_20200313_null_1,epi_isl_426167_South_Korea_20200223_null_4)Node44,epi_isl_423770_England_20200322_null_1,epi_isl_422581_Netherlands_20200330_null_1,epi_isl_416677_Washington_20200312_null_1,epi_isl_421889_England_20200327_null_1,((epi_isl_422636_Prague_20200308_null_1,epi_isl_422985_Washington_20200317_null_1)Node35,epi_isl_422275_Wales_20200330_null_4)Node34,epi_isl_423187_England_20200329_null_6,(epi_isl_407073_England_20200129_null_1,epi_isl_414480_USA_20200221_null_1)Node74,epi_isl_423536_England_20200331_null_1,epi_isl_417222_England_20200304_null_1,epi_isl_424600_Reykjavik_20200327_null_1,epi_isl_423043_Bangkok_20200318_null_2,epi_isl_421291_Wisconsin_20200323_null_2,(((((epi_isl_415435_Wales_20200306_null_1,epi_isl_424288_Washington_20200322_null_3)Node58,epi_isl_426093_Washington_20200325_null_8)Node57,((epi_isl_422425_Zhejiang_20200124_null_1,epi_isl_424315_Idaho_20200320_null_1)Node63,epi_isl_418999_Singapore_20200301_null_4)Node62)Node56,epi_isl_414937_Shandong_20200126_null_1)Node55,epi_isl_421881_England_20200326_null_4)Node54,epi_isl_422359_Wales_20200324_null_1,epi_isl_423309_England_20200325_null_1,epi_isl_422206_Wales_20200330_null_1,(epi_isl_423534_England_20200331_null_3,epi_isl_423904_England_20200318_null_1)Node93,epi_isl_426014_Scotland_20200401_null_10,epi_isl_425750_Scotland_20200319_null_2,epi_isl_423807_England_20200324_null_2,epi_isl_414934_Shandong_20200121_null_1,epi_isl_416373_Shanghai_20200207_null_1,epi_isl_425131_Duesseldorf_20200320_null_1,(epi_isl_425251_England_20200331_null_1,epi_isl_426103_Washington_20200323_null_2)Node84,epi_isl_422725_Netherlands_20200323_null_8,epi_isl_426135_Washington_20200330_null_8379,epi_isl_424366_Kayseri_20200317_null_3,(epi_isl_419835_Northern_Territory_20200224_null_17,(epi_isl_418182_Madrid_20200312_null_3,epi_isl_416567_unknown_20200215_null_1,epi_isl_424479_Reykjavik_20200320_null_1)Node14,epi_isl_416604_unknown_20200216_null_1)Node12,epi_isl_422051_Wales_20200330_null_1)"
}
},
"tested":{
"0":{
"Node1":"test",
"Node12":"test",
"Node14":"test",
"Node34":"test",
"Node35":"test",
"Node44":"test",
"Node54":"test",
"Node55":"test",
"Node56":"test",
"Node57":"test",
"Node58":"test",
"Node62":"test",
"Node63":"test",
"Node74":"test",
"Node84":"test",
"Node93":"test",
"epi_isl_407073_England_20200129_null_1":"test",
"epi_isl_414480_USA_20200221_null_1":"test",
"epi_isl_414934_Shandong_20200121_null_1":"test",
"epi_isl_414937_Shandong_20200126_null_1":"test",
"epi_isl_415435_Wales_20200306_null_1":"test",
"epi_isl_416373_Shanghai_20200207_null_1":"test",
"epi_isl_416567_unknown_20200215_null_1":"test",
"epi_isl_416604_unknown_20200216_null_1":"test",
"epi_isl_416677_Washington_20200312_null_1":"test",
"epi_isl_417222_England_20200304_null_1":"test",
"epi_isl_418113_Wales_20200313_null_1":"test",
"epi_isl_418182_Madrid_20200312_null_3":"test",
"epi_isl_418999_Singapore_20200301_null_4":"test",
"epi_isl_419835_Northern_Territory_20200224_null_17":"test",
"epi_isl_421291_Wisconsin_20200323_null_2":"test",
"epi_isl_421562_Utah_20200319_null_1":"test",
"epi_isl_421881_England_20200326_null_4":"test",
"epi_isl_421889_England_20200327_null_1":"test",
"epi_isl_422051_Wales_20200330_null_1":"test",
"epi_isl_422206_Wales_20200330_null_1":"test",
"epi_isl_422275_Wales_20200330_null_4":"test",
"epi_isl_422359_Wales_20200324_null_1":"test",
"epi_isl_422425_Zhejiang_20200124_null_1":"test",
"epi_isl_422581_Netherlands_20200330_null_1":"test",
"epi_isl_422636_Prague_20200308_null_1":"test",
"epi_isl_422725_Netherlands_20200323_null_8":"test",
"epi_isl_422985_Washington_20200317_null_1":"test",
"epi_isl_423043_Bangkok_20200318_null_2":"test",
"epi_isl_423187_England_20200329_null_6":"test",
"epi_isl_423309_England_20200325_null_1":"test",
"epi_isl_423534_England_20200331_null_3":"test",
"epi_isl_423536_England_20200331_null_1":"test",
"epi_isl_423770_England_20200322_null_1":"test",
"epi_isl_423807_England_20200324_null_2":"test",
"epi_isl_423904_England_20200318_null_1":"test",
"epi_isl_424158_England_20200321_null_1":"test",
"epi_isl_424288_Washington_20200322_null_3":"test",
"epi_isl_424315_Idaho_20200320_null_1":"test",
"epi_isl_424366_Kayseri_20200317_null_3":"test",
"epi_isl_424479_Reykjavik_20200320_null_1":"test",
"epi_isl_424600_Reykjavik_20200327_null_1":"test",
"epi_isl_425131_Duesseldorf_20200320_null_1":"test",
"epi_isl_425251_England_20200331_null_1":"test",
"epi_isl_425750_Scotland_20200319_null_2":"test",
"epi_isl_426014_Scotland_20200401_null_10":"test",
"epi_isl_426093_Washington_20200325_null_8":"test",
"epi_isl_426103_Washington_20200323_null_2":"test",
"epi_isl_426135_Washington_20200330_null_8379":"test",
"epi_isl_426167_South_Korea_20200223_null_4":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}