{
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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":{
"Node100":{
"Global MG94xREV":0.008066331916514782,
"Nucleotide GTR":0.007861911740597369,
"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", "F", "H", "A", "F"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTT", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TTT", "CAC", "GCC", "TTT"]
],
"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, 1, 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]
]
},
"Node101":{
"Global MG94xREV":0.5505977735606176,
"Nucleotide GTR":0.5366443068677135,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "F", "L", "V", "L", "I", "-", "P", "I", "I", "L", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "V", "F"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TTT", "CTT", "GTT", "TTA", "ATT", "---", "CCA", "ATT", "ATT", "CTT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "GTT", "TTT"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 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, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0]
]
},
"Node103":{
"Global MG94xREV":0.4967979855267859,
"Nucleotide GTR":0.4842079343550909,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "F", "L", "V", "L", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "V", "F"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TTT", "CTT", "GTT", "TTA", "ATT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "GTT", "TTT"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"Node104":{
"Global MG94xREV":1.415958864018835,
"Nucleotide GTR":1.380075074079329,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "F", "I", "T", "L", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TTT", "ATA", "ACA", "CTC", "ATT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 1, 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, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"Node11":{
"Global MG94xREV":0.004695389999419084,
"Nucleotide GTR":0.004576397567714539,
"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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"Nucleotide GTR":0.00405185941844375,
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"Nucleotide GTR":0.007805985929276667,
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"Nucleotide GTR":0.8339094268021439,
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"Nucleotide GTR":270.3689178821649,
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"original name":"epi_isl_413752_China_20200201_null_1",
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"Nucleotide GTR":0.007804580113191161,
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"original name":"epi_isl_414509_North_Rhine_Westphalia_20200228_null_2",
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"Nucleotide GTR":0.007766028888840724,
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"Nucleotide GTR":0.007821026474107843,
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"epi_isl_418004_Portugal_20200312_null_1":{
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"Nucleotide GTR":0.00380485609911033,
"amino-acid": [
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"epi_isl_418035_Connecticut_20200314_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_418035_Connecticut_20200314_null_1",
"synonymous substitution count": [
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"epi_isl_418052_Washington_20200316_null_1":{
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"Nucleotide GTR":0.3112386782934642,
"amino-acid": [
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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":0.3128999620643122,
"Nucleotide GTR":0.3049703273862768,
"amino-acid": [
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"codon": [
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"synonymous substitution count": [
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"epi_isl_418078_Washington_20200315_null_1":{
"Global MG94xREV":0.4148604986291909,
"Nucleotide GTR":0.4043469396796351,
"amino-acid": [
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"nonsynonymous substitution count": [
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"synonymous substitution count": [
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"epi_isl_418638_Li_ge_20200319_null_1":{
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"Nucleotide GTR":0.007768702959938281,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_418638_Li_ge_20200319_null_1",
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"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "T", "N", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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]
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"epi_isl_419431_Wales_20200317_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "ILVF", "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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"original name":"epi_isl_419431_Wales_20200317_null_1",
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]
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"epi_isl_419575_Luxembourg_20200314_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "CW", "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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"original name":"epi_isl_419575_Luxembourg_20200314_null_1",
"synonymous substitution count": [
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]
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"epi_isl_420106_Singapore_20200306_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_420106_Singapore_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_420388_Vilvoorde_20200324_null_1":{
"Global MG94xREV":0.008023097672947708,
"Nucleotide GTR":0.007819773156342011,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_420388_Vilvoorde_20200324_null_1",
"synonymous substitution count": [
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]
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"epi_isl_421952_England_20200331_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_421952_England_20200331_null_1",
"synonymous substitution count": [
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"epi_isl_421996_England_20200401_null_1":{
"Global MG94xREV":0.008010589062071553,
"Nucleotide GTR":0.007807581543633317,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_421996_England_20200401_null_1",
"synonymous substitution count": [
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"epi_isl_422349_Wales_20200324_null_2":{
"Global MG94xREV":0.00470072937563613,
"Nucleotide GTR":0.004581601631346276,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_422349_Wales_20200324_null_2",
"synonymous substitution count": [
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]
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"epi_isl_422464_Wisconsin_20200326_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_422464_Wisconsin_20200326_null_1",
"synonymous substitution count": [
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]
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"epi_isl_422580_Netherlands_20200330_null_1":{
"Global MG94xREV":0.008007340654959663,
"Nucleotide GTR":0.007804415458940105,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_422580_Netherlands_20200330_null_1",
"synonymous substitution count": [
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]
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"epi_isl_422998_Washington_20200317_null_1":{
"Global MG94xREV":0.4104958899009439,
"Nucleotide GTR":0.400092940593202,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_422998_Washington_20200317_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423009_Washington_20200318_null_1":{
"Global MG94xREV":0.008082668930287275,
"Nucleotide GTR":0.007877834735300987,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_423009_Washington_20200318_null_1",
"synonymous substitution count": [
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"epi_isl_423024_Washington_20200317_null_1":{
"Global MG94xREV":0.3330209217417301,
"Nucleotide GTR":0.3245813737400853,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_423024_Washington_20200317_null_1",
"synonymous substitution count": [
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"epi_isl_423058_England_20200324_null_1":{
"Global MG94xREV":0.007970711289276776,
"Nucleotide GTR":0.007768714369139511,
"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, 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]
],
"original name":"epi_isl_423058_England_20200324_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_423141_England_20200323_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "LF", "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", "TTN", "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, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_423141_England_20200323_null_1",
"synonymous substitution count": [
[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]
]
},
"epi_isl_423152_England_20200324_null_1":{
"Global MG94xREV":0.00386765295407972,
"Nucleotide GTR":0.003769637362179545,
"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", "TGT", "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_423152_England_20200324_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_423277_England_20200306_null_1":{
"Global MG94xREV":0.008021831891153646,
"Nucleotide GTR":0.007818539452491132,
"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", "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, 0, 0, 1, 0]
],
"original name":"epi_isl_423277_England_20200306_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_423428_England_20200330_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", "KQE", "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, 1, 0, 0, 0, 0, 0]
],
"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", "KQE", "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, 1, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423468_England_20200330_null_2",
"synonymous substitution count": [
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]
},
"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", "NHDY", "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, 3, 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": [
["IM", "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": [
[3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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", "YSCF", "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, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"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":0.007975816575424741,
"Nucleotide GTR":0.00777369027510535,
"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": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_423881_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["MLV", "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": [
[3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423881_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"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", "KN", "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, 1, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_423896_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, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_424002_England_20200320_null_2":{
"Global MG94xREV":0.008021372723617784,
"Nucleotide GTR":0.007818091921360694,
"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": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 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]
]
},
"epi_isl_424220_Washington_20200321_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "P", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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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]
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"original name":"epi_isl_424220_Washington_20200321_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424374_Reykjavik_20200301_null_1":{
"Global MG94xREV":0.008075035294908273,
"Nucleotide GTR":0.007870394554531002,
"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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],
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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, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"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":0.008026649755170492,
"Nucleotide GTR":0.007823235220291245,
"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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"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, 0, 0, 0, 0]
],
"original name":"epi_isl_424396_Reykjavik_20200319_null_3",
"synonymous substitution count": [
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]
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"epi_isl_424964_New_York_20200401_null_3":{
"Global MG94xREV":0.008007980266955095,
"Nucleotide GTR":0.007805038861635211,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_424964_New_York_20200401_null_3",
"synonymous substitution count": [
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]
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"epi_isl_425245_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", "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", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425245_England_20200331_null_1",
"synonymous substitution count": [
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]
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"epi_isl_425436_England_20200401_null_1":{
"Global MG94xREV":0.008031104639396292,
"Nucleotide GTR":0.007827577207077852,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425436_England_20200401_null_1",
"synonymous substitution count": [
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]
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"epi_isl_425725_Scotland_20200318_null_2":{
"Global MG94xREV":0.003949476477038308,
"Nucleotide GTR":0.003849387281035236,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_425725_Scotland_20200318_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_425745_Scotland_20200319_null_2":{
"Global MG94xREV":0.007963686246364449,
"Nucleotide GTR":0.007761867357645042,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_425745_Scotland_20200319_null_2",
"synonymous substitution count": [
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]
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"epi_isl_426930_Victoria_20200328_null_1":{
"Global MG94xREV":0.008008194120611918,
"Nucleotide GTR":0.007805247295728022,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_426930_Victoria_20200328_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_427031_Victoria_20200330_null_1":{
"Global MG94xREV":0.0080672067123151,
"Nucleotide GTR":0.007862764366976291,
"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", "S", "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, 1, 0, 0, 0]
],
"original name":"epi_isl_427031_Victoria_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_427266_Washington_20200330_null_1":{
"Global MG94xREV":0.008038987184561707,
"Nucleotide GTR":0.007835259989663937,
"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", "Y", "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_427266_Washington_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_428477_Guangdong_20200128_null_3":{
"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", "V", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_428477_Guangdong_20200128_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_428830_Singapore_20200227_null_16":{
"Global MG94xREV":0.008578529940403852,
"Nucleotide GTR":0.008361129439447543,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_428830_Singapore_20200227_null_16",
"synonymous substitution count": [
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]
},
"epi_isl_429103_Guangzhou_20200209_null_1":{
"Global MG94xREV":0.007978352710210699,
"Nucleotide GTR":0.007776162138159814,
"amino-acid": [
["R", "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_429103_Guangzhou_20200209_null_1",
"synonymous substitution count": [
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]
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"epi_isl_429168_Bangkok_20200317_null_13":{
"Global MG94xREV":0.008033716644173239,
"Nucleotide GTR":0.007830123017395956,
"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", "F", "H", "A", "-"]
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"codon": [
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"original name":"epi_isl_429168_Bangkok_20200317_null_13",
"synonymous substitution count": [
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]
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"epi_isl_429566_Unknown_20200323_null_1":{
"Global MG94xREV":0.00800829920662484,
"Nucleotide GTR":0.00780534971860961,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429566_Unknown_20200323_null_1",
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"epi_isl_429645_Connecticut_20200406_null_1":{
"Global MG94xREV":0.003809363371645171,
"Nucleotide GTR":0.00371282497741288,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429645_Connecticut_20200406_null_1",
"synonymous substitution count": [
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"epi_isl_429783_Luxembourg_20200327_null_1":{
"Global MG94xREV":0.007969636876298968,
"Nucleotide GTR":0.007767667184360619,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429783_Luxembourg_20200327_null_1",
"synonymous substitution count": [
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"epi_isl_429845_Iowa_20200414_null_1":{
"Global MG94xREV":0.007964157300490616,
"Nucleotide GTR":0.007762326474131125,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429845_Iowa_20200414_null_1",
"synonymous substitution count": [
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"epi_isl_429990_California_20200321_null_1":{
"Global MG94xREV":0.009132171016849207,
"Nucleotide GTR":0.008900739924613821,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429990_California_20200321_null_1",
"synonymous substitution count": [
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"epi_isl_430137_Washington_20200321_null_1":{
"Global MG94xREV":0.007985793738869812,
"Nucleotide GTR":0.007783414593325643,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430137_Washington_20200321_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430366_New_York_20200408_null_3":{
"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_430366_New_York_20200408_null_3",
"synonymous substitution count": [
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]
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"epi_isl_430427_New_York_20200413_null_1":{
"Global MG94xREV":0.007964911571820756,
"Nucleotide GTR":0.007763061630418677,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_430427_New_York_20200413_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430628_Victoria_20200411_null_2":{
"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_430628_Victoria_20200411_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_430715_Victoria_20200417_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_430715_Victoria_20200417_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_430716_Victoria_20200412_null_8":{
"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_430716_Victoria_20200412_null_8",
"synonymous substitution count": [
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]
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"epi_isl_430896_Washington_20200329_null_1":{
"Global MG94xREV":0.4094214168796739,
"Nucleotide GTR":0.3990456972924914,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430896_Washington_20200329_null_1",
"synonymous substitution count": [
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]
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"epi_isl_430912_Washington_20200408_null_11":{
"Global MG94xREV":0.003797416355147252,
"Nucleotide GTR":0.00370118072693543,
"amino-acid": [
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"Global MG94xREV":0.008007517785168259,
"Nucleotide GTR":0.007804588100244861,
"amino-acid": [
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.003864260234047309,
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"epi_isl_433307_Scotland_20200324_null_1":{
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"Nucleotide GTR":0.003207247531434267,
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"epi_isl_433631_Scotland_20200405_null_1":{
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"Nucleotide GTR":0.007828211786953507,
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"epi_isl_433792_England_20200407_null_2":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_433792_England_20200407_null_2",
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"epi_isl_433953_England_20200413_null_1":{
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"Nucleotide GTR":0.007818092110534667,
"amino-acid": [
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"original name":"epi_isl_433953_England_20200413_null_1",
"synonymous substitution count": [
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"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
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"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
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"amino-acid":{
"attribute type":"node label",
"display order":1
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"codon":{
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"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
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"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
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}
}
},
"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"
}
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"fits":{
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"Equilibrium frequencies": [
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[0.01099931307556225],
[0.008205623072782281],
[0.02202381863157493],
[0.006040452745884651],
[0.004694719288456806],
[0.003502318431065116],
[0.009400191214199436],
[0.004012060394331836],
[0.003118226085380087],
[0.002326235078188143],
[0.006243594057635864],
[0.02997088193234089],
[0.0232937634675951],
[0.01737743454055297],
[0.04664087823783456],
[0.01548409521944806],
[0.01203444237529555],
[0.008977842283823371],
[0.0240964480586076],
[0.0066089109375886],
[0.005136532468618182],
[0.003831916506880063],
[0.01028482948952338],
[0.004389629542327032],
[0.003411677791136233],
[0.002545153666190683],
[0.006831169581698243],
[0.03279139788764548],
[0.0254859055496253],
[0.01901279954230828],
[0.0510301832151191],
[0.0123014629260072],
[0.009560858714490987],
[0.007132518396766205],
[0.01914361531884105],
[0.00525050199755408],
[0.0040807591813034],
[0.003044296626756364],
[0.0081708648049884],
[0.003487376195285806],
[0.002710434627812918],
[0.002022017626597365],
[0.005427077149782886],
[0.02605138754895879],
[0.0202474809028985],
[0.01510487021518386],
[0.04054133599874095],
[0.02202853701975392],
[0.04410752750732074],
[0.01209733153467791],
[0.009402205113416794],
[0.007014160855653315],
[0.0188259447414786],
[0.0062449316867223],
[0.004658795979756971],
[0.01250416656841244],
[0.06002326487352007],
[0.04665087059076013],
[0.03480212422859454],
[0.09340858886712389]
],
"Log Likelihood":-550.6570692948677,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.6545657663189907, 1]
]
},
"display order":1,
"estimated parameters":112
},
"Nucleotide GTR":{
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"Equilibrium frequencies": [
[0.2250263496896592],
[0.1861459187258461],
[0.1312214545028692],
[0.4576062770816255]
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"Log Likelihood":-559.384109053541,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.1442662479713767,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.1807765474321005,
"Substitution rate from nucleotide C to nucleotide G":0.3366228882400604,
"Substitution rate from nucleotide C to nucleotide T":0.9349936983227871,
"Substitution rate from nucleotide G to nucleotide T":0.5645141248876677
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"display order":0,
"estimated parameters":157
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-01/sequences.ORF7b.compressed.fas",
"number of sequences":76,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_430715_Victoria_20200417_null_1,epi_isl_432044_Wales_20200408_null_1,epi_isl_423669_England_20200320_null_1,epi_isl_420106_Singapore_20200306_null_1,epi_isl_423141_England_20200323_null_1,epi_isl_419431_Wales_20200317_null_1,(epi_isl_423896_England_20200318_null_1,epi_isl_430912_Washington_20200408_null_11)Node88,(epi_isl_419575_Luxembourg_20200314_null_1,epi_isl_423152_England_20200324_null_1)Node50,(epi_isl_432041_Wales_20200401_null_1,epi_isl_418004_Portugal_20200312_null_1)Node47,epi_isl_426930_Victoria_20200328_null_1,epi_isl_429783_Luxembourg_20200327_null_1,epi_isl_425436_England_20200401_null_1,epi_isl_430137_Washington_20200321_null_1,(epi_isl_418991_Hangzhou_20200204_null_1,epi_isl_423024_Washington_20200317_null_1)Node36,epi_isl_433953_England_20200413_null_1,epi_isl_418638_Li_ge_20200319_null_1,epi_isl_423823_England_20200322_null_1,epi_isl_423567_England_20200401_null_1,(epi_isl_421952_England_20200331_null_1,epi_isl_429645_Connecticut_20200406_null_1)Node85,epi_isl_424374_Reykjavik_20200301_null_1,epi_isl_430931_Washington_20200407_null_8,epi_isl_429566_Unknown_20200323_null_1,epi_isl_427266_Washington_20200330_null_1,(epi_isl_423826_England_20200322_null_2,epi_isl_425725_Scotland_20200318_null_2)Node20,(epi_isl_418052_Washington_20200316_null_1,epi_isl_430366_New_York_20200408_null_3)Node61,epi_isl_421996_England_20200401_null_1,epi_isl_417453_Washington_20200314_null_1,epi_isl_424396_Reykjavik_20200319_null_3,(epi_isl_432607_England_20200404_null_1,epi_isl_423881_England_20200318_null_1)Node17,epi_isl_417253_England_20200303_null_1,epi_isl_424964_New_York_20200401_null_3,epi_isl_433631_Scotland_20200405_null_1,((epi_isl_422998_Washington_20200317_null_1,epi_isl_422464_Wisconsin_20200326_null_1)Node76,epi_isl_428477_Guangdong_20200128_null_3)Node75,epi_isl_423277_England_20200306_null_1,epi_isl_429845_Iowa_20200414_null_1,epi_isl_425745_Scotland_20200319_null_2,(epi_isl_433307_Scotland_20200324_null_1,epi_isl_429990_California_20200321_null_1)Node11,epi_isl_429103_Guangzhou_20200209_null_1,((epi_isl_433792_England_20200407_null_2,epi_isl_425245_England_20200331_null_1)Node140,epi_isl_423531_England_20200326_null_1)Node139,epi_isl_430969_Washington_20200402_null_14064,epi_isl_422580_Netherlands_20200330_null_1,epi_isl_414509_North_Rhine_Westphalia_20200228_null_2,epi_isl_423428_England_20200330_null_1,epi_isl_423468_England_20200330_null_2,epi_isl_420388_Vilvoorde_20200324_null_1,((epi_isl_418078_Washington_20200315_null_1,epi_isl_428830_Singapore_20200227_null_16)Node128,epi_isl_432471_England_20200323_null_1)Node127,epi_isl_424002_England_20200320_null_2,(epi_isl_422349_Wales_20200324_null_2,epi_isl_423009_Washington_20200318_null_1)Node118,epi_isl_423058_England_20200324_null_1,epi_isl_430427_New_York_20200413_null_1,epi_isl_427031_Victoria_20200330_null_1,(((epi_isl_424220_Washington_20200321_null_1,((epi_isl_418035_Connecticut_20200314_null_1,epi_isl_430896_Washington_20200329_null_1)Node104,epi_isl_413752_China_20200201_null_1)Node103,epi_isl_413747_China_20200201_null_1,epi_isl_418065_Washington_20200313_null_1)Node101,epi_isl_430628_Victoria_20200411_null_2)Node100,epi_isl_430716_Victoria_20200412_null_8)Node99,epi_isl_429168_Bangkok_20200317_null_13)"
}
},
"tested":{
"0":{
"Node100":"test",
"Node101":"test",
"Node103":"test",
"Node104":"test",
"Node11":"test",
"Node118":"test",
"Node127":"test",
"Node128":"test",
"Node139":"test",
"Node140":"test",
"Node17":"test",
"Node20":"test",
"Node36":"test",
"Node47":"test",
"Node50":"test",
"Node61":"test",
"Node75":"test",
"Node76":"test",
"Node85":"test",
"Node88":"test",
"Node99":"test",
"epi_isl_413747_China_20200201_null_1":"test",
"epi_isl_413752_China_20200201_null_1":"test",
"epi_isl_414509_North_Rhine_Westphalia_20200228_null_2":"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_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_422464_Wisconsin_20200326_null_1":"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_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_1":"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_2":"test",
"epi_isl_426930_Victoria_20200328_null_1":"test",
"epi_isl_427031_Victoria_20200330_null_1":"test",
"epi_isl_427266_Washington_20200330_null_1":"test",
"epi_isl_428477_Guangdong_20200128_null_3":"test",
"epi_isl_428830_Singapore_20200227_null_16":"test",
"epi_isl_429103_Guangzhou_20200209_null_1":"test",
"epi_isl_429168_Bangkok_20200317_null_13":"test",
"epi_isl_429566_Unknown_20200323_null_1":"test",
"epi_isl_429645_Connecticut_20200406_null_1":"test",
"epi_isl_429783_Luxembourg_20200327_null_1":"test",
"epi_isl_429845_Iowa_20200414_null_1":"test",
"epi_isl_429990_California_20200321_null_1":"test",
"epi_isl_430137_Washington_20200321_null_1":"test",
"epi_isl_430366_New_York_20200408_null_3":"test",
"epi_isl_430427_New_York_20200413_null_1":"test",
"epi_isl_430628_Victoria_20200411_null_2":"test",
"epi_isl_430715_Victoria_20200417_null_1":"test",
"epi_isl_430716_Victoria_20200412_null_8":"test",
"epi_isl_430896_Washington_20200329_null_1":"test",
"epi_isl_430912_Washington_20200408_null_11":"test",
"epi_isl_430931_Washington_20200407_null_8":"test",
"epi_isl_430969_Washington_20200402_null_14064":"test",
"epi_isl_432041_Wales_20200401_null_1":"test",
"epi_isl_432044_Wales_20200408_null_1":"test",
"epi_isl_432471_England_20200323_null_1":"test",
"epi_isl_432607_England_20200404_null_1":"test",
"epi_isl_433307_Scotland_20200324_null_1":"test",
"epi_isl_433631_Scotland_20200405_null_1":"test",
"epi_isl_433792_England_20200407_null_2":"test",
"epi_isl_433953_England_20200413_null_1":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}