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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":{
"Node105":{
"Global MG94xREV":0.006558804694481397,
"Nucleotide GTR":0.006381889607888784,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "I", "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", "ATA", "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, 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]
],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"Node106":{
"Global MG94xREV":0.002570919670593344,
"Nucleotide GTR":0.002501572510960988,
"amino-acid": [
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],
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
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"Global MG94xREV":0.009816383012922047,
"Nucleotide GTR":0.009551599057360971,
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["-", "-", "-", "-", "-", "-", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "I", "M", "N", "S", "R", "N", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
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],
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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, 0, 0, 0]
]
},
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"Global MG94xREV":62.66179584505449,
"Nucleotide GTR":60.9715767343522,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "I", "I", "I", "I", "I", "I", "-", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "I", "I", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
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["---", "---", "---", "---", "---", "---", "ATT", "ATT", "ATT", "ATT", "ATT", "ATT", "---", "ATT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "ATT", "ATT", "ATT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
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[0, 0, 0, 0, 0, 0, 1, 2, 1, 2.333333333333333, 1, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 1, 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, 1, 0, 0, 0.6666666666666666, 0, 0.5, 0, 1, 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]
]
},
"Node110":{
"Global MG94xREV":245.5177344781017,
"Nucleotide GTR":238.8952181388421,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "K", "K", "K", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "AAA", "AAA", "AAA", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
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]
},
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"Global MG94xREV":0.5209939396575384,
"Nucleotide GTR":0.5069408168337575,
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],
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],
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"Nucleotide GTR":0.02221401949340513,
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"Nucleotide GTR":1.005385041465696,
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"Nucleotide GTR":0.007081118512822795,
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"Nucleotide GTR":0.001088752101797956,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.008841327166835713,
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"Nucleotide GTR":2.925936479564761,
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"epi_isl_415435_Wales_20200306_null_1":{
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"Nucleotide GTR":4.991615406235211,
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"Nucleotide GTR":6.427479915582499e-05,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.03229668334296175,
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"codon": [
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"Nucleotide GTR":0.001431802586639373,
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"Nucleotide GTR":0.008849432664017779,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.008782857549355165,
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"Nucleotide GTR":0.008794268152302597,
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"Nucleotide GTR":0,
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"epi_isl_424288_Washington_20200322_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_424315_Idaho_20200320_null_1":{
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"Nucleotide GTR":0.3369360480544593,
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"epi_isl_424366_Kayseri_20200317_null_3":{
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"Nucleotide GTR":0.008853252547961352,
"amino-acid": [
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"Nucleotide GTR":0.008786417650072618,
"amino-acid": [
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"Global MG94xREV":0.009040147965289196,
"Nucleotide GTR":0.008796301924037986,
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"Nucleotide GTR":0.2722344470561973,
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"Nucleotide GTR":0.008858664440333265,
"amino-acid": [
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":16.91380806877519,
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"codon": [
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"original name":"epi_isl_428685_Madrid_20200327_null_1",
"synonymous substitution count": [
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"epi_isl_429689_Minas_gerais_20200317_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"epi_isl_430520_Victoria_20200402_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430520_Victoria_20200402_null_1",
"synonymous substitution count": [
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"epi_isl_430566_Victoria_20200406_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"epi_isl_430608_Victoria_20200408_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_430709_Victoria_20200407_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_430737_Beijing_20200225_null_5":{
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"Nucleotide GTR":0.008857230892041119,
"amino-acid": [
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"Nucleotide GTR":0.4482519324270689,
"amino-acid": [
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"codon": [
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"synonymous substitution count": [
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"epi_isl_430903_USA_20200405_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":0.008793653277459438,
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"Nucleotide GTR":0.00888036500509439,
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"Nucleotide GTR":0.008880877656183615,
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"epi_isl_433714_England_20200405_null_1":{
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"Nucleotide GTR":0.008907566774196267,
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"Nucleotide GTR":0.008857392260103798,
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"epi_isl_434332_Washington_20200326_null_1":{
"Global MG94xREV":0.009038940818936971,
"Nucleotide GTR":0.008795127338862891,
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"epi_isl_435058_KZN_20200311_null_1":{
"Global MG94xREV":0.009190511269135665,
"Nucleotide GTR":0.008942609376527457,
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"epi_isl_437478_Makkah_20200409_null_1":{
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"Nucleotide GTR":0.8901064699858052,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_437478_Makkah_20200409_null_1",
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"epi_isl_437867_Connecticut_20200402_null_1":{
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"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_437867_Connecticut_20200402_null_1",
"synonymous substitution count": [
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]
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"epi_isl_437869_Connecticut_20200403_null_11":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_437869_Connecticut_20200403_null_11",
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"epi_isl_438253_England_20200404_null_2":{
"Global MG94xREV":0.009040259547390225,
"Nucleotide GTR":0.008796410496359333,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_438253_England_20200404_null_2",
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"epi_isl_438977_Scotland_20200420_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"epi_isl_439881_England_20200323_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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]
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"epi_isl_440074_England_20200323_null_3":{
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"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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"original name":"epi_isl_440074_England_20200323_null_3",
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]
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"epi_isl_440493_England_20200310_null_4":{
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"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "Y", "S", "L", "L", "L", "C", "I", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-", "-", "-", "-"]
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],
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"original name":"epi_isl_440493_England_20200310_null_4",
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]
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"epi_isl_440730_England_20200402_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "V", "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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],
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"original name":"epi_isl_440730_England_20200402_null_1",
"synonymous substitution count": [
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]
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"epi_isl_441602_England_20200406_null_1":{
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"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", "IF", "N", "L", "T", "-", "-", "-", "-", "-", "-", "-", "-"]
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"original name":"epi_isl_441602_England_20200406_null_1",
"synonymous substitution count": [
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]
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"epi_isl_442129_England_20200407_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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]
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"epi_isl_442145_England_20200405_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"synonymous substitution count": [
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"epi_isl_442883_England_20200410_null_1":{
"Global MG94xREV":0.009041378639012896,
"Nucleotide GTR":0.0087974994019648,
"amino-acid": [
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"original name":"epi_isl_442883_England_20200410_null_1",
"synonymous substitution count": [
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"epi_isl_443363_England_20200414_null_2":{
"Global MG94xREV":0.009186558579528629,
"Nucleotide GTR":0.008938763305497541,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_443363_England_20200414_null_2",
"synonymous substitution count": [
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"epi_isl_443597_England_20200414_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_443597_England_20200414_null_1",
"synonymous substitution count": [
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"epi_isl_443691_England_20200330_null_2":{
"Global MG94xREV":0.009108922783758052,
"Nucleotide GTR":0.008863221632691634,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_443691_England_20200330_null_2",
"synonymous substitution count": [
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]
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"epi_isl_444065_California_20200430_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_444065_California_20200430_null_1",
"synonymous substitution count": [
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]
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"epi_isl_444149_England_20200409_null_4":{
"Global MG94xREV":0.009042500084252943,
"Nucleotide GTR":0.008798590597701932,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_444149_England_20200409_null_4",
"synonymous substitution count": [
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"epi_isl_444822_Unknown_20200311_null_6":{
"Global MG94xREV":0.002547248896687627,
"Nucleotide GTR":0.002478540224891134,
"amino-acid": [
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"codon": [
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"epi_isl_446256_Wales_20200417_null_2":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_446256_Wales_20200417_null_2",
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"epi_isl_446888_Wales_20200417_null_1":{
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"Nucleotide GTR":0.0005660903531930508,
"amino-acid": [
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"original name":"epi_isl_446888_Wales_20200417_null_1",
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"epi_isl_446927_Wales_20200417_null_17":{
"Global MG94xREV":0.009040147965289196,
"Nucleotide GTR":0.008796301924037986,
"amino-acid": [
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"original name":"epi_isl_446927_Wales_20200417_null_17",
"synonymous substitution count": [
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"epi_isl_447517_Comunitat_Valenciana_20200401_null_3":{
"Global MG94xREV":0.009127474551731482,
"Nucleotide GTR":0.008881272991247434,
"amino-acid": [
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],
"original name":"epi_isl_447517_Comunitat_Valenciana_20200401_null_3",
"synonymous substitution count": [
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]
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"epi_isl_447596_Kinshasa_20200405_null_10":{
"Global MG94xREV":0.009033936893105067,
"Nucleotide GTR":0.00879025838731564,
"amino-acid": [
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"original name":"epi_isl_447596_Kinshasa_20200405_null_10",
"synonymous substitution count": [
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]
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"epi_isl_448167_Scotland_20200411_null_4":{
"Global MG94xREV":0.00912641514534865,
"Nucleotide GTR":0.008880242160951355,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_448167_Scotland_20200411_null_4",
"synonymous substitution count": [
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"epi_isl_448447_England_20200427_null_1":{
"Global MG94xREV":0.008705289728726709,
"Nucleotide GTR":0.008470476045759857,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_448447_England_20200427_null_1",
"synonymous substitution count": [
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"epi_isl_448730_England_20200101_null_24":{
"Global MG94xREV":0.001812705787394307,
"Nucleotide GTR":0.001763810444983267,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_448730_England_20200101_null_24",
"synonymous substitution count": [
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"epi_isl_448967_Northern_Ireland_20200328_null_30":{
"Global MG94xREV":0.009096351116907717,
"Nucleotide GTR":0.008850989069936168,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_448967_Northern_Ireland_20200328_null_30",
"synonymous substitution count": [
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]
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"epi_isl_449194_Scotland_20200422_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_449194_Scotland_20200422_null_1",
"synonymous substitution count": [
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]
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"epi_isl_449262_Scotland_20200503_null_1":{
"Global MG94xREV":0.009125683232433162,
"Nucleotide GTR":0.008879529990419245,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_449262_Scotland_20200503_null_1",
"synonymous substitution count": [
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"epi_isl_449707_England_20200416_null_3":{
"Global MG94xREV":0.008285437717927448,
"Nucleotide GTR":0.00806194898795228,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_449707_England_20200416_null_3",
"synonymous substitution count": [
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"epi_isl_449727_England_20200417_null_3":{
"Global MG94xREV":0.009040752598741254,
"Nucleotide GTR":0.008796890248301941,
"amino-acid": [
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"codon": [
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]
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"Global MG94xREV":0.003013430749561071,
"Nucleotide GTR":0.002932147438526057,
"amino-acid": [
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],
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]
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"epi_isl_450500_Hubei_20200110_null_1":{
"Global MG94xREV":0.009106997101329882,
"Nucleotide GTR":0.008861347893001416,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_450500_Hubei_20200110_null_1",
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]
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"epi_isl_450547_Utah_20200403_null_24":{
"Global MG94xREV":0.009096948415376024,
"Nucleotide GTR":0.008851570257067863,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_450547_Utah_20200403_null_24",
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]
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"epi_isl_450635_Michigan_20200330_null_17":{
"Global MG94xREV":0.009103900632254183,
"Nucleotide GTR":0.008858334947085822,
"amino-acid": [
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],
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],
"original name":"epi_isl_450635_Michigan_20200330_null_17",
"synonymous substitution count": [
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]
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"epi_isl_450703_Illinois_20200415_null_19":{
"Global MG94xREV":0.009024609415180749,
"Nucleotide GTR":0.008781182505778416,
"amino-acid": [
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],
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],
"original name":"epi_isl_450703_Illinois_20200415_null_19",
"synonymous substitution count": [
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]
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"epi_isl_450842_Dhaka_20200506_null_3":{
"Global MG94xREV":0.2588223270999464,
"Nucleotide GTR":0.2518409369619662,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_450842_Dhaka_20200506_null_3",
"synonymous substitution count": [
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]
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"epi_isl_450843_Dhaka_20200506_null_2":{
"Global MG94xREV":0.009108614390113319,
"Nucleotide GTR":0.008862921557557786,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_450843_Dhaka_20200506_null_2",
"synonymous substitution count": [
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]
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"epi_isl_451370_Sichuan_20200204_null_5":{
"Global MG94xREV":0.009101349108058075,
"Nucleotide GTR":0.008855852246882052,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_451370_Sichuan_20200204_null_5",
"synonymous substitution count": [
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]
},
"epi_isl_451762_Vaud_20200326_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_451762_Vaud_20200326_null_2",
"synonymous substitution count": [
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]
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"epi_isl_451777_Schwyz_20200326_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_451777_Schwyz_20200326_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_451826_Bern_20200331_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_451826_Bern_20200331_null_1",
"synonymous substitution count": [
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"epi_isl_451893_Bern_20200407_null_2":{
"Global MG94xREV":0.009096352421797457,
"Nucleotide GTR":0.008850990339628231,
"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", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_451893_Bern_20200407_null_2",
"synonymous substitution count": [
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"epi_isl_451901_Valais_20200407_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.008785815551127138,
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"Nucleotide GTR":0,
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"epi_isl_452536_Navarra_20200311_null_3":{
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"Nucleotide GTR":0,
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"epi_isl_452945_England_20200515_null_2":{
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"Nucleotide GTR":0.008795293058280805,
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"original name":"epi_isl_452945_England_20200515_null_2",
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"epi_isl_453009_Scotland_20200403_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_453009_Scotland_20200403_null_1",
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"epi_isl_453064_Scotland_20200416_null_5":{
"Global MG94xREV":0.009130048295071214,
"Nucleotide GTR":0.008883777311262796,
"amino-acid": [
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"original name":"epi_isl_453064_Scotland_20200416_null_5",
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"epi_isl_453192_Scotland_20200424_null_7":{
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"Nucleotide GTR":0.008849609629137186,
"amino-acid": [
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"original name":"epi_isl_453192_Scotland_20200424_null_7",
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"epi_isl_453574_England_20200424_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_453574_England_20200424_null_1",
"synonymous substitution count": [
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"epi_isl_453703_England_20200423_null_46":{
"Global MG94xREV":0.003146943919054906,
"Nucleotide GTR":0.003062059266762983,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_453703_England_20200423_null_46",
"synonymous substitution count": [
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"epi_isl_453741_England_20200422_null_1":{
"Global MG94xREV":0.001526152897204525,
"Nucleotide GTR":0.001484986940213965,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_453741_England_20200422_null_1",
"synonymous substitution count": [
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"epi_isl_453857_Portugal_20200327_null_1":{
"Global MG94xREV":0.2038842385378903,
"Nucleotide GTR":0.198384730716572,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_453857_Portugal_20200327_null_1",
"synonymous substitution count": [
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"epi_isl_453882_Portugal_20200328_null_1":{
"Global MG94xREV":0.3096666985422508,
"Nucleotide GTR":0.301313848695457,
"amino-acid": [
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"Nucleotide GTR":1.962261644011023,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.008853797878359434,
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"Nucleotide GTR":0.003029143675072776,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.008848972436347035,
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"original name":"epi_isl_454499_Nur_Sultan_20200416_null_21",
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
}
},
"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"amino-acid":{
"attribute type":"node label",
"display order":1
},
"codon":{
"attribute type":"node label",
"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
"attribute type":"branch label",
"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":inf,
"Equilibrium frequencies": [
[0.0307025821637209],
[0.02316276587048153],
[0.01455635503110585],
[0.03655985640388873],
[0.0162384830615251],
[0.01225070188690287],
[0.007698802770063544],
[0.01933637391736527],
[0.01503852711026394],
[0.01134542627829964],
[0.007129893459598923],
[0.01790749679441963],
[0.04527972114771815],
[0.03416010985761923],
[0.0214675004604166],
[0.05391794391563565],
[0.0133442820029647],
[0.01006724705095268],
[0.006326637461127788],
[0.01589003267672588],
[0.007057741792460867],
[0.005324530029472662],
[0.00334613534135668],
[0.008404179983694974],
[0.006536204205837759],
[0.00493106953982429],
[0.003098869940926529],
[0.007783146248665936],
[0.01967995280620816],
[0.01484702937236863],
[0.009330432812295297],
[0.02343438883392862],
[0.0175852487650479],
[0.01326673430094372],
[0.008337315831266573],
[0.02094006837107335],
[0.009300773553221177],
[0.007016727097377145],
[0.004409575754334524],
[0.01107512533433255],
[0.008613485305037237],
[0.006498220325102175],
[0.004083726557158734],
[0.01025671991397752],
[0.02593446883876442],
[0.01956558658435645],
[0.01229575199724684],
[0.03088210794780411],
[0.01993755757678333],
[0.03146922289537044],
[0.01397741931205934],
[0.01054490105334974],
[0.006626813238053505],
[0.01664395653176229],
[0.009765676988732055],
[0.006137119468458767],
[0.01541403778768075],
[0.03897492434587896],
[0.0294036196248686],
[0.01847834273559839],
[0.04641035173652224]
],
"Log Likelihood":-inf,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.9165418920175951, 1]
]
},
"display order":1,
"estimated parameters":153
},
"Nucleotide GTR":{
"AIC-c":2285.633808549774,
"Equilibrium frequencies": [
[0.2990862230552952],
[0.183622305529522],
[0.1593017806935332],
[0.3579896907216494]
],
"Log Likelihood":-908.4036184969111,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.1254499370054293,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.1060491465153968,
"Substitution rate from nucleotide C to nucleotide G":0.8151294449215072,
"Substitution rate from nucleotide C to nucleotide T":1.551663103438946,
"Substitution rate from nucleotide G to nucleotide T":0.5667647045076165
},
"display order":0,
"estimated parameters":231
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-28/sequences.ORF10.compressed.fas",
"number of sequences":113,
"number of sites":47,
"partition count":1,
"trees":{
"0":"(epi_isl_440074_England_20200323_null_3,epi_isl_451893_Bern_20200407_null_2,epi_isl_433319_Scotland_20200325_null_1,epi_isl_427272_Arizona_20200323_null_3,epi_isl_451370_Sichuan_20200204_null_5,(epi_isl_423904_England_20200318_null_1,epi_isl_444822_Unknown_20200311_null_6)Node23,epi_isl_449194_Scotland_20200422_null_1,epi_isl_451913_Vaud_20200407_null_2,(epi_isl_414937_Shandong_20200126_null_1,epi_isl_446888_Wales_20200417_null_1)Node33,epi_isl_449727_England_20200417_null_3,epi_isl_424600_Reykjavik_20200327_null_1,epi_isl_451777_Schwyz_20200326_null_1,epi_isl_417222_England_20200304_null_1,epi_isl_450547_Utah_20200403_null_24,(epi_isl_421889_England_20200327_null_1,epi_isl_448730_England_20200101_null_24)Node64,epi_isl_422051_Wales_20200330_null_1,epi_isl_434251_Washington_20200402_null_1,epi_isl_453574_England_20200424_null_1,epi_isl_454308_Portugal_20200327_null_1,epi_isl_454499_Nur_Sultan_20200416_null_21,(((epi_isl_437869_Connecticut_20200403_null_11,epi_isl_453857_Portugal_20200327_null_1)Node54,epi_isl_450842_Dhaka_20200506_null_3)Node53,epi_isl_416604_unknown_20200216_null_1)Node52,epi_isl_424158_England_20200321_null_1,epi_isl_423770_England_20200322_null_1,epi_isl_448167_Scotland_20200411_null_4,(epi_isl_450252_Saint_Petersburg_20200420_null_1,epi_isl_451901_Valais_20200407_null_3)Node220,epi_isl_423536_England_20200331_null_1,epi_isl_430520_Victoria_20200402_null_1,(epi_isl_450703_Illinois_20200415_null_19,epi_isl_440730_England_20200402_null_1,epi_isl_451826_Bern_20200331_null_1)Node195,epi_isl_442145_England_20200405_null_1,epi_isl_444149_England_20200409_null_4,epi_isl_425251_England_20200331_null_1,((epi_isl_453950_Portugal_20200331_null_14,epi_isl_454016_Portugal_20200313_null_2)Node205,epi_isl_416567_unknown_20200215_null_1)Node204,epi_isl_454259_Portugal_20200407_null_1,epi_isl_430709_Victoria_20200407_null_1,epi_isl_443691_England_20200330_null_2,epi_isl_453064_Scotland_20200416_null_5,epi_isl_441602_England_20200406_null_1,(epi_isl_439881_England_20200323_null_1,epi_isl_454428_Maryland_20200312_null_22)Node186,epi_isl_433714_England_20200405_null_1,epi_isl_452945_England_20200515_null_2,epi_isl_454097_Portugal_20200320_null_4,(epi_isl_452536_Navarra_20200311_null_3,epi_isl_453703_England_20200423_null_46)Node165,epi_isl_451762_Vaud_20200326_null_2,epi_isl_448967_Northern_Ireland_20200328_null_30,epi_isl_435058_KZN_20200311_null_1,epi_isl_446256_Wales_20200417_null_2,((epi_isl_426103_Washington_20200323_null_2,epi_isl_430896_Washington_20200329_null_1)Node174,epi_isl_453908_Portugal_20200329_null_2)Node173,epi_isl_444065_California_20200430_null_1,(epi_isl_452466_Andalusia_20200311_null_1,epi_isl_453990_Portugal_20200405_null_6)Node157,epi_isl_447517_Comunitat_Valenciana_20200401_null_3,epi_isl_432653_England_20200318_null_1,epi_isl_443363_England_20200414_null_2,epi_isl_442883_England_20200410_null_1,epi_isl_453192_Scotland_20200424_null_7,epi_isl_424366_Kayseri_20200317_null_3,epi_isl_437478_Makkah_20200409_null_1,epi_isl_438977_Scotland_20200420_null_1,epi_isl_426949_Victoria_20200328_null_1,epi_isl_449262_Scotland_20200503_null_1,epi_isl_454495_Sormland_20200308_null_31752,epi_isl_438253_England_20200404_null_2,epi_isl_432289_Wales_20200401_null_1,epi_isl_430566_Victoria_20200406_null_1,epi_isl_450500_Hubei_20200110_null_1,epi_isl_414480_USA_20200221_null_1,epi_isl_452292_Michigan_20200316_null_2,epi_isl_442129_England_20200407_null_1,epi_isl_447596_Kinshasa_20200405_null_10,(epi_isl_448447_England_20200427_null_1,epi_isl_449707_England_20200416_null_3,epi_isl_453882_Portugal_20200328_null_1)Node87,epi_isl_434332_Washington_20200326_null_1,epi_isl_414934_Shandong_20200121_null_1,epi_isl_446927_Wales_20200417_null_17,epi_isl_418182_Madrid_20200312_null_3,epi_isl_443597_England_20200414_null_1,epi_isl_454176_Portugal_20200404_null_1,(epi_isl_453009_Scotland_20200403_null_1,epi_isl_453741_England_20200422_null_1)Node133,epi_isl_422206_Wales_20200330_null_1,epi_isl_433486_England_20200417_null_1,epi_isl_454396_Pennsylvania_20200101_null_2,epi_isl_430608_Victoria_20200408_null_1,epi_isl_450635_Michigan_20200330_null_17,epi_isl_430737_Beijing_20200225_null_5,((epi_isl_440493_England_20200310_null_4,((((epi_isl_422425_Zhejiang_20200124_null_1,epi_isl_424315_Idaho_20200320_null_1)Node111,epi_isl_418999_Singapore_20200301_null_4)Node110,epi_isl_428685_Madrid_20200327_null_1)Node109,(epi_isl_424288_Washington_20200322_null_1,epi_isl_430903_USA_20200405_null_3,epi_isl_437867_Connecticut_20200402_null_1)Node116)Node108,(epi_isl_429689_Minas_gerais_20200317_null_1,epi_isl_453928_Portugal_20200330_null_1)Node121)Node106,epi_isl_415435_Wales_20200306_null_1)Node105,epi_isl_450843_Dhaka_20200506_null_2)"
}
},
"tested":{
"0":{
"Node105":"test",
"Node106":"test",
"Node108":"test",
"Node109":"test",
"Node110":"test",
"Node111":"test",
"Node116":"test",
"Node121":"test",
"Node133":"test",
"Node157":"test",
"Node165":"test",
"Node173":"test",
"Node174":"test",
"Node186":"test",
"Node195":"test",
"Node204":"test",
"Node205":"test",
"Node220":"test",
"Node23":"test",
"Node33":"test",
"Node52":"test",
"Node53":"test",
"Node54":"test",
"Node64":"test",
"Node87":"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_416567_unknown_20200215_null_1":"test",
"epi_isl_416604_unknown_20200216_null_1":"test",
"epi_isl_417222_England_20200304_null_1":"test",
"epi_isl_418182_Madrid_20200312_null_3":"test",
"epi_isl_418999_Singapore_20200301_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_422425_Zhejiang_20200124_null_1":"test",
"epi_isl_423536_England_20200331_null_1":"test",
"epi_isl_423770_England_20200322_null_1":"test",
"epi_isl_423904_England_20200318_null_1":"test",
"epi_isl_424158_England_20200321_null_1":"test",
"epi_isl_424288_Washington_20200322_null_1":"test",
"epi_isl_424315_Idaho_20200320_null_1":"test",
"epi_isl_424366_Kayseri_20200317_null_3":"test",
"epi_isl_424600_Reykjavik_20200327_null_1":"test",
"epi_isl_425251_England_20200331_null_1":"test",
"epi_isl_426103_Washington_20200323_null_2":"test",
"epi_isl_426949_Victoria_20200328_null_1":"test",
"epi_isl_427272_Arizona_20200323_null_3":"test",
"epi_isl_428685_Madrid_20200327_null_1":"test",
"epi_isl_429689_Minas_gerais_20200317_null_1":"test",
"epi_isl_430520_Victoria_20200402_null_1":"test",
"epi_isl_430566_Victoria_20200406_null_1":"test",
"epi_isl_430608_Victoria_20200408_null_1":"test",
"epi_isl_430709_Victoria_20200407_null_1":"test",
"epi_isl_430737_Beijing_20200225_null_5":"test",
"epi_isl_430896_Washington_20200329_null_1":"test",
"epi_isl_430903_USA_20200405_null_3":"test",
"epi_isl_432289_Wales_20200401_null_1":"test",
"epi_isl_432653_England_20200318_null_1":"test",
"epi_isl_433319_Scotland_20200325_null_1":"test",
"epi_isl_433486_England_20200417_null_1":"test",
"epi_isl_433714_England_20200405_null_1":"test",
"epi_isl_434251_Washington_20200402_null_1":"test",
"epi_isl_434332_Washington_20200326_null_1":"test",
"epi_isl_435058_KZN_20200311_null_1":"test",
"epi_isl_437478_Makkah_20200409_null_1":"test",
"epi_isl_437867_Connecticut_20200402_null_1":"test",
"epi_isl_437869_Connecticut_20200403_null_11":"test",
"epi_isl_438253_England_20200404_null_2":"test",
"epi_isl_438977_Scotland_20200420_null_1":"test",
"epi_isl_439881_England_20200323_null_1":"test",
"epi_isl_440074_England_20200323_null_3":"test",
"epi_isl_440493_England_20200310_null_4":"test",
"epi_isl_440730_England_20200402_null_1":"test",
"epi_isl_441602_England_20200406_null_1":"test",
"epi_isl_442129_England_20200407_null_1":"test",
"epi_isl_442145_England_20200405_null_1":"test",
"epi_isl_442883_England_20200410_null_1":"test",
"epi_isl_443363_England_20200414_null_2":"test",
"epi_isl_443597_England_20200414_null_1":"test",
"epi_isl_443691_England_20200330_null_2":"test",
"epi_isl_444065_California_20200430_null_1":"test",
"epi_isl_444149_England_20200409_null_4":"test",
"epi_isl_444822_Unknown_20200311_null_6":"test",
"epi_isl_446256_Wales_20200417_null_2":"test",
"epi_isl_446888_Wales_20200417_null_1":"test",
"epi_isl_446927_Wales_20200417_null_17":"test",
"epi_isl_447517_Comunitat_Valenciana_20200401_null_3":"test",
"epi_isl_447596_Kinshasa_20200405_null_10":"test",
"epi_isl_448167_Scotland_20200411_null_4":"test",
"epi_isl_448447_England_20200427_null_1":"test",
"epi_isl_448730_England_20200101_null_24":"test",
"epi_isl_448967_Northern_Ireland_20200328_null_30":"test",
"epi_isl_449194_Scotland_20200422_null_1":"test",
"epi_isl_449262_Scotland_20200503_null_1":"test",
"epi_isl_449707_England_20200416_null_3":"test",
"epi_isl_449727_England_20200417_null_3":"test",
"epi_isl_450252_Saint_Petersburg_20200420_null_1":"test",
"epi_isl_450500_Hubei_20200110_null_1":"test",
"epi_isl_450547_Utah_20200403_null_24":"test",
"epi_isl_450635_Michigan_20200330_null_17":"test",
"epi_isl_450703_Illinois_20200415_null_19":"test",
"epi_isl_450842_Dhaka_20200506_null_3":"test",
"epi_isl_450843_Dhaka_20200506_null_2":"test",
"epi_isl_451370_Sichuan_20200204_null_5":"test",
"epi_isl_451762_Vaud_20200326_null_2":"test",
"epi_isl_451777_Schwyz_20200326_null_1":"test",
"epi_isl_451826_Bern_20200331_null_1":"test",
"epi_isl_451893_Bern_20200407_null_2":"test",
"epi_isl_451901_Valais_20200407_null_3":"test",
"epi_isl_451913_Vaud_20200407_null_2":"test",
"epi_isl_452292_Michigan_20200316_null_2":"test",
"epi_isl_452466_Andalusia_20200311_null_1":"test",
"epi_isl_452536_Navarra_20200311_null_3":"test",
"epi_isl_452945_England_20200515_null_2":"test",
"epi_isl_453009_Scotland_20200403_null_1":"test",
"epi_isl_453064_Scotland_20200416_null_5":"test",
"epi_isl_453192_Scotland_20200424_null_7":"test",
"epi_isl_453574_England_20200424_null_1":"test",
"epi_isl_453703_England_20200423_null_46":"test",
"epi_isl_453741_England_20200422_null_1":"test",
"epi_isl_453857_Portugal_20200327_null_1":"test",
"epi_isl_453882_Portugal_20200328_null_1":"test",
"epi_isl_453908_Portugal_20200329_null_2":"test",
"epi_isl_453928_Portugal_20200330_null_1":"test",
"epi_isl_453950_Portugal_20200331_null_14":"test",
"epi_isl_453990_Portugal_20200405_null_6":"test",
"epi_isl_454016_Portugal_20200313_null_2":"test",
"epi_isl_454097_Portugal_20200320_null_4":"test",
"epi_isl_454176_Portugal_20200404_null_1":"test",
"epi_isl_454259_Portugal_20200407_null_1":"test",
"epi_isl_454308_Portugal_20200327_null_1":"test",
"epi_isl_454396_Pennsylvania_20200101_null_2":"test",
"epi_isl_454428_Maryland_20200312_null_22":"test",
"epi_isl_454495_Sormland_20200308_null_31752":"test",
"epi_isl_454499_Nur_Sultan_20200416_null_21":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":2
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":4
}
}
}