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[2.058097054144505, 1.153903064266663, 0, 0, 0.6407524838954717, 0, 0, 0, 1, 1, 1.24135768129258],
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[5.743952909872991, 17.49259567568305, 0, 0, 0.247194753933614, 0, 0, 0, 1, 1, 0.3050639301427256],
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[4.461518691881072, 18.77502989367498, 0, 0, 0.1920043622422641, 0, 0, 0, 1, 1, 0.3050639301427256],
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[0.9874303480074488, 2.224569770403721, 0, 0, 0.3074191505621381, 0, 0, 0, 1, 1, 1.24135768129258],
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[0.5524720594224958, 2.091059912429128, 0, 0, 0.208990118260429, 0, 0, 0, 1, 1, 1.24135768129258],
[2.058097054144505, 1.153903064266663, 0, 0, 0.6407524838954717, 0, 0, 0, 1, 1, 1.24135768129258],
[0.5524720594224958, 1.672097710981225, 0, 0, 0.2483500705497008, 0, 0, 0, 1, 1, 1.24135768129258],
[0.6167180342576132, 2.595282084153556, 0, 0, 0.1920043622422641, 0, 0, 0, 1, 1, 1.24135768129258],
[0.4576566020394754, 1.925917378753842, 0, 0, 0.1920043622422641, 0, 0, 0, 1, 1, 1.67279935568659],
[0.4576566020394754, 1.925917378753842, 0, 0, 0.1920043622422641, 0, 0, 0, 1, 1, 1.67279935568659],
[0.4099806903513286, 1.551742159340728, 0, 0, 0.208990118260429, 0, 0, 0, 1, 1, 1.67279935568659],
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[7.745516195185348, 15.4910323903707, 0, 0, 0.3333333333333334, 0, 0, 0, 1, 1, 0.3050639301427256],
[1.24025824772103, 5.219273365191584, 0, 0, 0.1920043622422641, 0, 0, 0, 1, 1, 0.7858721239141901]
]
}
}
},
"headers": [
["ES", "Expected synonymous sites"],
["EN", "Expected non-synonymous sites"],
["S", "Inferred synonymous substitutions"],
["N", "Inferred non-synonymous substitutions"],
["P[S]", "Expected proportion of synonymous sites"],
["dS", "Inferred synonymous susbsitution rate"],
["dN", "Inferred non-synonymous susbsitution rate"],
["dN-dS", "Scaled by the length of the tested branches"],
["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"],
["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
]
},
"analysis":{
"authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
"citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
"contact":"spond@temple.edu",
"info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.00"
},
"branch attributes":{
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"Node98":{
"Global MG94xREV":0.02763783029159407,
"Nucleotide GTR":0.02355014098986827,
"amino-acid": [
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"Nucleotide GTR":0.7338572540779679,
"amino-acid": [
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"Nucleotide GTR":146.7685650149343,
"amino-acid": [
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"Global MG94xREV":0.007599263615504789,
"Nucleotide GTR":0.007816391472922448,
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"Nucleotide GTR":0.7328941077453933,
"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":{
"Global MG94xREV":0.4535933946050829,
"Nucleotide GTR":0.4665535663917885,
"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":1.065974651799424,
"Nucleotide GTR":1.096431917650092,
"amino-acid": [
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"codon": [
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"epi_isl_418638_Li_ge_20200319_null_1":{
"Global MG94xREV":0.007556762738876856,
"Nucleotide GTR":0.007772676251754375,
"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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"epi_isl_418991_Hangzhou_20200204_null_1":{
"Global MG94xREV":4.479773317872638e-05,
"Nucleotide GTR":4.607770401727174e-05,
"amino-acid": [
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"codon": [
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"epi_isl_419431_Wales_20200317_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_419431_Wales_20200317_null_1",
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"epi_isl_419575_Luxembourg_20200314_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_420106_Singapore_20200306_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_420388_Vilvoorde_20200324_null_1":{
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"Nucleotide GTR":0.0078117604690326,
"amino-acid": [
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"codon": [
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"epi_isl_421952_England_20200331_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_421996_England_20200401_null_1":{
"Global MG94xREV":0.007586219148767552,
"Nucleotide GTR":0.007802974296767942,
"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", "F", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "TTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
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"synonymous substitution count": [
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]
},
"epi_isl_422349_Wales_20200324_null_2":{
"Global MG94xREV":0.0050642184197249,
"Nucleotide GTR":0.005208914399573056,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "ILVF", "F", "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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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
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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_422998_Washington_20200317_null_1":{
"Global MG94xREV":0.3649546201812316,
"Nucleotide GTR":0.3753821851064627,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "K", "ED", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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"original name":"epi_isl_422998_Washington_20200317_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423009_Washington_20200318_null_1":{
"Global MG94xREV":0.007655523537208202,
"Nucleotide GTR":0.007874258865675167,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "Y", "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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"nonsynonymous substitution count": [
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"original name":"epi_isl_423009_Washington_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423024_Washington_20200317_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "E", "A", "EDAGV", "-", "-", "-"]
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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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]
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"epi_isl_423058_England_20200324_null_1":{
"Global MG94xREV":0.007557409252168533,
"Nucleotide GTR":0.007773341237368223,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_423058_England_20200324_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423141_England_20200323_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_423141_England_20200323_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423152_England_20200324_null_1":{
"Global MG94xREV":0.003895117810424134,
"Nucleotide GTR":0.004006409986529355,
"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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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423152_England_20200324_null_1",
"synonymous substitution count": [
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]
},
"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", "KE", "T", "C", "H", "A", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_423428_England_20200330_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423468_England_20200330_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"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", "HY", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423531_England_20200326_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423567_England_20200401_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["MI", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_423567_England_20200401_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423669_England_20200320_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "YF", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_423669_England_20200320_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_423823_England_20200322_null_1":{
"Global MG94xREV":0.007558222462510607,
"Nucleotide GTR":0.007774177682937835,
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
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"original name":"epi_isl_423823_England_20200322_null_1",
"synonymous substitution count": [
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]
},
"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", "-"]
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"codon": [
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[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]
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"original name":"epi_isl_423826_England_20200322_null_2",
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]
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"epi_isl_423881_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["ML", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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"codon": [
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],
"original name":"epi_isl_423881_England_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423896_England_20200318_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
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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_423896_England_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_424002_England_20200320_null_2":{
"Global MG94xREV":0.007595550310308989,
"Nucleotide GTR":0.007812572070341183,
"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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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_424002_England_20200320_null_2",
"synonymous substitution count": [
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]
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"epi_isl_424220_Washington_20200321_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "P", "I", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424220_Washington_20200321_null_1",
"synonymous substitution count": [
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]
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"epi_isl_424374_Reykjavik_20200301_null_1":{
"Global MG94xREV":0.007651008744581738,
"Nucleotide GTR":0.007869615075385339,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424374_Reykjavik_20200301_null_1",
"synonymous substitution count": [
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]
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"epi_isl_426930_Victoria_20200328_null_1":{
"Global MG94xREV":0.007581728278180576,
"Nucleotide GTR":0.007798355112023467,
"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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]
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"epi_isl_427266_Washington_20200330_null_1":{
"Global MG94xREV":0.007611865731999424,
"Nucleotide GTR":0.007829353659904415,
"amino-acid": [
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"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":0.007588111869739925,
"Nucleotide GTR":0.0078049210969867,
"amino-acid": [
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"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":0.01065754991540662,
"Nucleotide GTR":0.01096205981209353,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"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,
"Nucleotide GTR":0,
"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", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429103_Guangzhou_20200209_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_429645_Connecticut_20200406_null_1":{
"Global MG94xREV":0.003848586207639728,
"Nucleotide GTR":0.003958548872396747,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "L", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429645_Connecticut_20200406_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_429783_Luxembourg_20200327_null_1":{
"Global MG94xREV":0.007561223293392691,
"Nucleotide GTR":0.007777264254230166,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_429783_Luxembourg_20200327_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_429845_Iowa_20200414_null_1":{
"Global MG94xREV":0.007551700369552456,
"Nucleotide GTR":0.007767469239282888,
"amino-acid": [
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"codon": [
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]
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"epi_isl_429990_California_20200321_null_1":{
"Global MG94xREV":0.007338202314508164,
"Nucleotide GTR":0.007547871070122274,
"amino-acid": [
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"codon": [
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"epi_isl_430137_Washington_20200321_null_1":{
"Global MG94xREV":0.007557115609507892,
"Nucleotide GTR":0.007773039204683896,
"amino-acid": [
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"original name":"epi_isl_430137_Washington_20200321_null_1",
"synonymous substitution count": [
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"epi_isl_430628_Victoria_20200411_null_2":{
"Global MG94xREV":0.0006171587887532212,
"Nucleotide GTR":0.0006347923875160092,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_430628_Victoria_20200411_null_2",
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"epi_isl_430715_Victoria_20200417_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_430715_Victoria_20200417_null_1",
"synonymous substitution count": [
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"Global MG94xREV":0.6649290642018409,
"Nucleotide GTR":0.6839275659448665,
"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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"epi_isl_432041_Wales_20200401_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_432041_Wales_20200401_null_1",
"synonymous substitution count": [
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]
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"epi_isl_432044_Wales_20200408_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_432044_Wales_20200408_null_1",
"synonymous substitution count": [
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"epi_isl_432420_Wales_20200330_null_2":{
"Global MG94xREV":0.007587836077520896,
"Nucleotide GTR":0.007804637424770794,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_432420_Wales_20200330_null_2",
"synonymous substitution count": [
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"epi_isl_432607_England_20200404_null_1":{
"Global MG94xREV":0.007553096973549909,
"Nucleotide GTR":0.007768905747361712,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_432607_England_20200404_null_1",
"synonymous substitution count": [
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"epi_isl_432900_England_20200302_null_2":{
"Global MG94xREV":7.265965910661671e-06,
"Nucleotide GTR":7.473570711610126e-06,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_432900_England_20200302_null_2",
"synonymous substitution count": [
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"epi_isl_433307_Scotland_20200324_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_433307_Scotland_20200324_null_1",
"synonymous substitution count": [
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]
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"epi_isl_433953_England_20200413_null_1":{
"Global MG94xREV":0.007594490611694659,
"Nucleotide GTR":0.00781148209378134,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_433953_England_20200413_null_1",
"synonymous substitution count": [
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"epi_isl_435144_Madrid_20200311_null_1":{
"Global MG94xREV":0.00755987381888789,
"Nucleotide GTR":0.007775876222238376,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_435144_Madrid_20200311_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_435402_Iowa_20200426_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAR", "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_435402_Iowa_20200426_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, 1, 0, 0, 0, 0, 0]
]
},
"epi_isl_435415_Baranya_20200330_null_1":{
"Global MG94xREV":0.007561116187093485,
"Nucleotide GTR":0.007777154087665848,
"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", "P", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CCT", "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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_435415_Baranya_20200330_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_435634_California_20200310_null_1":{
"Global MG94xREV":0.007625169563747425,
"Nucleotide GTR":0.007843037611704715,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "T", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "I", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "ACC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ATT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_435634_California_20200310_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_435686_Singapore_20200413_null_2":{
"Global MG94xREV":0.007596559649421508,
"Nucleotide GTR":0.007813610248516272,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "S", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "TCC", "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, 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]
],
"original name":"epi_isl_435686_Singapore_20200413_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_436118_Victoria_20200411_null_10":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_436118_Victoria_20200411_null_10",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_436418_Tamil_Nadu_20200331_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", "SL", "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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_436418_Tamil_Nadu_20200331_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_436517_Florida_20200408_null_1":{
"Global MG94xREV":0.3434329618277784,
"Nucleotide GTR":0.3532456051233895,
"amino-acid": [
["-", "-", "-", "-", "-", "P", "I", "QHPRL", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "CCT", "ATT", "C??", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 31.83333333333333, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_436517_Florida_20200408_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 1, 0, 8.166666666666668, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_436725_Abruzzo_20200427_null_1":{
"Global MG94xREV":0.007559230650074601,
"Nucleotide GTR":0.007775214676662098,
"amino-acid": [
["K", "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": [
["AAG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[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_436725_Abruzzo_20200427_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_437074_California_20200421_null_1":{
"Global MG94xREV":0.00755195674253787,
"Nucleotide GTR":0.007767732937414512,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAG", "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_437074_California_20200421_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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_437154_Michigan_20200322_null_2":{
"Global MG94xREV":0.003861233622805891,
"Nucleotide GTR":0.003971557652334002,
"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", "L", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TTA", "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_437154_Michigan_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_437301_Styria_20200417_null_2":{
"Global MG94xREV":0.007598207996457823,
"Nucleotide GTR":0.007815305692492287,
"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", "Y", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "TAT", "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, 1, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_437301_Styria_20200417_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_437384_Minnesota_20200416_null_8":{
"Global MG94xREV":0.007553819183128645,
"Nucleotide GTR":0.007769648592073848,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTG", "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_437384_Minnesota_20200416_null_8",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_437476_Makkah_20200409_null_1":{
"Global MG94xREV":1.181102431770558,
"Nucleotide GTR":1.214849154265867,
"amino-acid": [
["M", "K", "D", "L", "S", "P", "R", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["ATG", "AAA", "GAT", "CTC", "AGT", "CCA", "AGA", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 1.5, 1, 0, 2.25, 1.5, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_437476_Makkah_20200409_null_1",
"synonymous substitution count": [
[0, 0.5, 0, 1, 0.75, 0.5, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_437478_Makkah_20200409_null_1":{
"Global MG94xREV":0.7943579054307991,
"Nucleotide GTR":0.8170544769350506,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "Y", "Q", "E", "YSCWLF", "-", "-", "-", "-"]
],
"codon": [
["---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TAC", "CAA", "GAG", "T??", "---", "---", "---", "---"]
],
"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, 1, 2, 0, 23, 0, 0, 0, 0]
],
"original name":"epi_isl_437478_Makkah_20200409_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_437636_Unknown_20200331_null_2":{
"Global MG94xREV":0.007581937405971121,
"Nucleotide GTR":0.007798570215059952,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "V", "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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"original name":"epi_isl_437636_Unknown_20200331_null_2",
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]
},
"epi_isl_437860_Washington_20200404_null_17":{
"Global MG94xREV":0.007558496374253443,
"Nucleotide GTR":0.007774459420948176,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_437860_Washington_20200404_null_17",
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]
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"epi_isl_437867_Connecticut_20200402_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "L", "I", "T", "QHPRL", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
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"codon": [
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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_438106_Vienna_20200325_null_6":{
"Global MG94xREV":0.007555089935834047,
"Nucleotide GTR":0.007770955653009382,
"amino-acid": [
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],
"original name":"epi_isl_438106_Vienna_20200325_null_6",
"synonymous substitution count": [
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]
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"epi_isl_438536_England_20200401_null_2":{
"Global MG94xREV":0.007612829113496274,
"Nucleotide GTR":0.007830344567352572,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_438536_England_20200401_null_2",
"synonymous substitution count": [
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]
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"epi_isl_438844_Scotland_20200405_null_2":{
"Global MG94xREV":0.007607197203520578,
"Nucleotide GTR":0.007824551741187102,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_438844_Scotland_20200405_null_2",
"synonymous substitution count": [
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]
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"epi_isl_439249_Scotland_20200426_null_3":{
"Global MG94xREV":0.004124859797645346,
"Nucleotide GTR":0.004242716213125345,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_439249_Scotland_20200426_null_3",
"synonymous substitution count": [
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]
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"epi_isl_439286_Scotland_20200414_null_5":{
"Global MG94xREV":0.003864908239108535,
"Nucleotide GTR":0.003975337260594421,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_439286_Scotland_20200414_null_5",
"synonymous substitution count": [
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]
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"epi_isl_439341_Scotland_20200430_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_439341_Scotland_20200430_null_1",
"synonymous substitution count": [
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]
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"epi_isl_439507_England_20200330_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_439507_England_20200330_null_1",
"synonymous substitution count": [
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]
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"epi_isl_439984_England_20200320_null_5":{
"Global MG94xREV":0.003883838397231061,
"Nucleotide GTR":0.003994808295423129,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_439984_England_20200320_null_5",
"synonymous substitution count": [
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]
},
"epi_isl_440124_England_20200321_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_440124_England_20200321_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_440219_England_20200309_null_2":{
"Global MG94xREV":0.007561065089833775,
"Nucleotide GTR":0.007777101530443821,
"amino-acid": [
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"codon": [
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],
"original name":"epi_isl_440219_England_20200309_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_440525_England_20200310_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAY", "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_440525_England_20200310_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, 1, 0, 0]
]
},
"epi_isl_440875_England_20200423_null_4":{
"Global MG94xREV":0.007592747352887136,
"Nucleotide GTR":0.007809689026193793,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTT", "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_440875_England_20200423_null_4",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_441112_England_20200331_null_4":{
"Global MG94xREV":0.003870153031585152,
"Nucleotide GTR":0.003980731908453177,
"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", "Y", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "TAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_441112_England_20200331_null_4",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_441633_England_20200407_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "I", "E", "L", "S", "L", "I", "D", "F", "Y", "L", "C", "F", "L", "A", "F", "L", "L", "F", "L", "V", "L", "I", "M", "L", "I", "I", "F", "W", "F", "S", "L", "E", "L", "Q", "D", "H", "N", "E", "T", "C", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTR", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "GCC", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_441633_England_20200407_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_441767_England_20200407_null_12":{
"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", "I", "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_441767_England_20200407_null_12",
"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_442014_England_20200409_null_1":{
"Global MG94xREV":0.0008110329600893171,
"Nucleotide GTR":0.0008342059749798654,
"amino-acid": [
["I", "N", "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_442014_England_20200409_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_442155_England_20200404_null_1":{
"Global MG94xREV":0.0009605891424336889,
"Nucleotide GTR":0.0009880353099715198,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "M", "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", "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_442155_England_20200404_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_442776_England_20200406_null_3":{
"Global MG94xREV":0.0425296895418617,
"Nucleotide GTR":0.04374485733101716,
"amino-acid": [
["-", "-", "M", "I", "E", "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", "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, 2.333333333333333, 1, 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_442776_England_20200406_null_3",
"synonymous substitution count": [
[0, 0, 0.6666666666666666, 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_442896_England_20200408_null_7":{
"Global MG94xREV":0.007555941172019884,
"Nucleotide GTR":0.007771831210905648,
"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_442896_England_20200408_null_7",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_442980_England_20200412_null_12":{
"Global MG94xREV":0.007582239392063175,
"Nucleotide GTR":0.007798880829566079,
"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_442980_England_20200412_null_12",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_443051_England_20200412_null_3":{
"Global MG94xREV":0.007599369401457734,
"Nucleotide GTR":0.007816500281415274,
"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": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TGT", "CAC", "ACC", "---"]
],
"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_443051_England_20200412_null_3",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_443092_England_20200407_null_25":{
"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", "F", "H", "A", "-"]
],
"codon": [
["ATG", "ATT", "GAA", "CTT", "TCA", "TTA", "ATT", "GAC", "TTC", "TAT", "TTG", "TGC", "TTT", "TTA", "GCC", "TTT", "CTG", "CTA", "TTC", "CTT", "GTT", "TTA", "ATT", "ATG", "CTT", "ATT", "ATC", "TTT", "TGG", "TTC", "TCA", "CTT", "GAA", "CTG", "CAA", "GAT", "CAT", "AAT", "GAA", "ACT", "TTT", "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_443092_England_20200407_null_25",
"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_443306_Ile_de_France_20200402_null_1":{
"Global MG94xREV":0.007594711740875151,
"Nucleotide GTR":0.007811709541114167,
"amino-acid": [
["I", "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_443306_Ile_de_France_20200402_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_443368_England_20200416_null_2":{
"Global MG94xREV":0.007592904165156932,
"Nucleotide GTR":0.00780985031893878,
"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": [
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"original name":"epi_isl_443368_England_20200416_null_2",
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"Nucleotide GTR":0.007805281380180366,
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"original name":"epi_isl_443458_England_20200414_null_9",
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"Nucleotide GTR":0,
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"epi_isl_443761_England_20200325_null_1":{
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"Nucleotide GTR":0,
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"epi_isl_444068_California_20200430_null_2":{
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"Nucleotide GTR":0.007777640879744301,
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"epi_isl_444156_England_20200413_null_4":{
"Global MG94xREV":0.007587904675063018,
"Nucleotide GTR":0.007804707982297204,
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"original name":"epi_isl_444156_England_20200413_null_4",
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"epi_isl_444259_England_20200419_null_6":{
"Global MG94xREV":0.00758784890218805,
"Nucleotide GTR":0.007804650615867196,
"amino-acid": [
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"original name":"epi_isl_444259_England_20200419_null_6",
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"epi_isl_445040_Florida_20200428_null_3":{
"Global MG94xREV":0.284386164015852,
"Nucleotide GTR":0.2925117090155023,
"amino-acid": [
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"epi_isl_445136_Louisiana_20200331_null_22391":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_445136_Louisiana_20200331_null_22391",
"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":{
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"display order":1
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"original name":{
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"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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[0.01111154756312696],
[0.008253776870115066],
[0.02226098428399324],
[0.006056101047760878],
[0.004708926855600848],
[0.003497841443148566],
[0.009433910634992116],
[0.004028237600601331],
[0.003132159795323432],
[0.002326601935983586],
[0.006274999911806049],
[0.02991972570301565],
[0.02326410982313985],
[0.01728083063778128],
[0.04660754770762723],
[0.01569227339162681],
[0.01220154139049296],
[0.009063435991832389],
[0.02444468869805379],
[0.006650177860415624],
[0.005170851819424561],
[0.003840964267442536],
[0.01035933567607164],
[0.004423389949531512],
[0.00343941086218254],
[0.002554831328383919],
[0.006890549737942593],
[0.03285471888443287],
[0.02554621643001208],
[0.0189760039356435],
[0.05117954265444841],
[0.01239815395126003],
[0.009640195835660255],
[0.00716084100434346],
[0.01931326368114453],
[0.005254173621566403],
[0.004085387458938005],
[0.003034669682370632],
[0.008184705640754936],
[0.003494832661404619],
[0.002717410301666583],
[0.002018521557603467],
[0.005444086674236193],
[0.02595786171887108],
[0.02018355889341686],
[0.01499256432145516],
[0.04043594150758988],
[0.02211534710216145],
[0.04430610511086432],
[0.01205347643936149],
[0.009372191524057697],
[0.006961764523265624],
[0.01877634119264933],
[0.006233947221076319],
[0.004630642949644897],
[0.01248915151802403],
[0.05954932158319847],
[0.04630262893972215],
[0.0343940900758427],
[0.09276314476258775]
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"Log Likelihood":-752.5533420016782,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *background*": [
[0.6854805143405857, 1]
],
"non-synonymous/synonymous rate ratio for *test*": [
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"display order":1,
"estimated parameters":144
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"Nucleotide GTR":{
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"Equilibrium frequencies": [
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[0.1865992359784684],
[0.1311208543149852],
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"Log Likelihood":-764.2604398716334,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.1494557302043922,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.2083269019029687,
"Substitution rate from nucleotide C to nucleotide G":0,
"Substitution rate from nucleotide C to nucleotide T":0.8770102043595793,
"Substitution rate from nucleotide G to nucleotide T":0.5599243402010241
},
"display order":0,
"estimated parameters":211
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-15/sequences.ORF7b.compressed.fas",
"number of sequences":103,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_430715_Victoria_20200417_null_1,epi_isl_439507_England_20200330_null_1,epi_isl_420106_Singapore_20200306_null_1,epi_isl_423141_England_20200323_null_1,epi_isl_423669_England_20200320_null_1,(epi_isl_436418_Tamil_Nadu_20200331_null_2,epi_isl_437154_Michigan_20200322_null_2)Node196,(epi_isl_421952_England_20200331_null_1,epi_isl_429645_Connecticut_20200406_null_1)Node193,(epi_isl_432044_Wales_20200408_null_1,epi_isl_439286_Scotland_20200414_null_5)Node190,(epi_isl_439984_England_20200320_null_5,epi_isl_440525_England_20200310_null_2)Node187,(epi_isl_423531_England_20200326_null_1,epi_isl_441112_England_20200331_null_4)Node184,epi_isl_444156_England_20200413_null_4,(epi_isl_419575_Luxembourg_20200314_null_1,epi_isl_423152_England_20200324_null_1)Node130,(epi_isl_422349_Wales_20200324_null_2,epi_isl_423009_Washington_20200318_null_1)Node127,epi_isl_419431_Wales_20200317_null_1,epi_isl_429783_Luxembourg_20200327_null_1,epi_isl_423567_England_20200401_null_1,(((epi_isl_422998_Washington_20200317_null_1,epi_isl_442155_England_20200404_null_1)Node118,epi_isl_442014_England_20200409_null_1)Node117,epi_isl_433307_Scotland_20200324_null_1)Node116,epi_isl_443306_Ile_de_France_20200402_null_1,epi_isl_437636_Unknown_20200331_null_2,epi_isl_442980_England_20200412_null_12,epi_isl_440219_England_20200309_null_2,epi_isl_435144_Madrid_20200311_null_1,epi_isl_427266_Washington_20200330_null_1,epi_isl_421996_England_20200401_null_1,epi_isl_445136_Louisiana_20200331_null_22391,epi_isl_437860_Washington_20200404_null_17,epi_isl_423896_England_20200318_null_1,(epi_isl_423024_Washington_20200317_null_1,epi_isl_437478_Makkah_20200409_null_1)Node143,epi_isl_435402_Iowa_20200426_null_1,epi_isl_417453_Washington_20200314_null_1,epi_isl_440875_England_20200423_null_4,epi_isl_443761_England_20200325_null_1,(epi_isl_439249_Scotland_20200426_null_3,epi_isl_443634_England_20200413_null_1)Node177,epi_isl_443051_England_20200412_null_3,epi_isl_444259_England_20200419_null_6,epi_isl_429845_Iowa_20200414_null_1,(epi_isl_429103_Guangzhou_20200209_null_1,epi_isl_436725_Abruzzo_20200427_null_1)Node163,((epi_isl_442776_England_20200406_null_3,(epi_isl_424220_Washington_20200321_null_1,epi_isl_436517_Florida_20200408_null_1)Node169,epi_isl_429990_California_20200321_null_1)Node167,epi_isl_432900_England_20200302_null_2)Node166,epi_isl_432420_Wales_20200330_null_2,epi_isl_423881_England_20200318_null_1,epi_isl_432607_England_20200404_null_1,epi_isl_428477_Guangdong_20200128_null_3,(epi_isl_443092_England_20200407_null_25,epi_isl_443368_England_20200416_null_2)Node41,epi_isl_435415_Baranya_20200330_null_1,((((epi_isl_418035_Connecticut_20200314_null_1,epi_isl_430896_Washington_20200329_null_1,epi_isl_437867_Connecticut_20200402_null_1)Node32,epi_isl_413752_China_20200201_null_1,epi_isl_413747_China_20200201_null_1,epi_isl_418065_Washington_20200313_null_1)Node26,epi_isl_430628_Victoria_20200411_null_2)Node25,epi_isl_436118_Victoria_20200411_null_10)Node24,epi_isl_437384_Minnesota_20200416_null_8,epi_isl_426930_Victoria_20200328_null_1,epi_isl_424002_England_20200320_null_2,epi_isl_437301_Styria_20200417_null_2,epi_isl_437074_California_20200421_null_1,epi_isl_428830_Singapore_20200227_null_16,epi_isl_423826_England_20200322_null_2,epi_isl_437476_Makkah_20200409_null_1,epi_isl_443458_England_20200414_null_9,epi_isl_438536_England_20200401_null_2,epi_isl_423058_England_20200324_null_1,epi_isl_430137_Washington_20200321_null_1,epi_isl_438844_Scotland_20200405_null_2,(epi_isl_439341_Scotland_20200430_null_1,epi_isl_445040_Florida_20200428_null_3)Node65,epi_isl_441633_England_20200407_null_1,((epi_isl_435634_California_20200310_null_1,epi_isl_441767_England_20200407_null_12)Node80,epi_isl_440124_England_20200321_null_1)Node79,epi_isl_432041_Wales_20200401_null_1,epi_isl_435686_Singapore_20200413_null_2,epi_isl_438106_Vienna_20200325_null_6,epi_isl_418638_Li_ge_20200319_null_1,epi_isl_423823_England_20200322_null_1,epi_isl_444068_California_20200430_null_2,epi_isl_424374_Reykjavik_20200301_null_1,epi_isl_423428_England_20200330_null_1,epi_isl_420388_Vilvoorde_20200324_null_1,epi_isl_423468_England_20200330_null_2,epi_isl_442896_England_20200408_null_7,(epi_isl_418052_Washington_20200316_null_1,epi_isl_418991_Hangzhou_20200204_null_1)Node98,epi_isl_433953_England_20200413_null_1)"
}
},
"tested":{
"0":{
"Node116":"test",
"Node117":"test",
"Node118":"test",
"Node127":"test",
"Node130":"test",
"Node143":"test",
"Node163":"test",
"Node166":"test",
"Node167":"test",
"Node169":"test",
"Node177":"test",
"Node184":"test",
"Node187":"test",
"Node190":"test",
"Node193":"test",
"Node196":"test",
"Node24":"test",
"Node25":"test",
"Node26":"test",
"Node32":"test",
"Node41":"test",
"Node65":"test",
"Node79":"test",
"Node80":"test",
"Node98":"test",
"epi_isl_413747_China_20200201_null_1":"background",
"epi_isl_413752_China_20200201_null_1":"background",
"epi_isl_417453_Washington_20200314_null_1":"background",
"epi_isl_418035_Connecticut_20200314_null_1":"background",
"epi_isl_418052_Washington_20200316_null_1":"background",
"epi_isl_418065_Washington_20200313_null_1":"background",
"epi_isl_418638_Li_ge_20200319_null_1":"background",
"epi_isl_418991_Hangzhou_20200204_null_1":"background",
"epi_isl_419431_Wales_20200317_null_1":"background",
"epi_isl_419575_Luxembourg_20200314_null_1":"background",
"epi_isl_420106_Singapore_20200306_null_1":"background",
"epi_isl_420388_Vilvoorde_20200324_null_1":"background",
"epi_isl_421952_England_20200331_null_1":"background",
"epi_isl_421996_England_20200401_null_1":"background",
"epi_isl_422349_Wales_20200324_null_2":"background",
"epi_isl_422998_Washington_20200317_null_1":"background",
"epi_isl_423009_Washington_20200318_null_1":"background",
"epi_isl_423024_Washington_20200317_null_1":"background",
"epi_isl_423058_England_20200324_null_1":"background",
"epi_isl_423141_England_20200323_null_1":"background",
"epi_isl_423152_England_20200324_null_1":"background",
"epi_isl_423428_England_20200330_null_1":"background",
"epi_isl_423468_England_20200330_null_2":"background",
"epi_isl_423531_England_20200326_null_1":"background",
"epi_isl_423567_England_20200401_null_1":"background",
"epi_isl_423669_England_20200320_null_1":"background",
"epi_isl_423823_England_20200322_null_1":"background",
"epi_isl_423826_England_20200322_null_2":"background",
"epi_isl_423881_England_20200318_null_1":"background",
"epi_isl_423896_England_20200318_null_1":"background",
"epi_isl_424002_England_20200320_null_2":"background",
"epi_isl_424220_Washington_20200321_null_1":"background",
"epi_isl_424374_Reykjavik_20200301_null_1":"background",
"epi_isl_426930_Victoria_20200328_null_1":"background",
"epi_isl_427266_Washington_20200330_null_1":"background",
"epi_isl_428477_Guangdong_20200128_null_3":"background",
"epi_isl_428830_Singapore_20200227_null_16":"background",
"epi_isl_429103_Guangzhou_20200209_null_1":"background",
"epi_isl_429645_Connecticut_20200406_null_1":"background",
"epi_isl_429783_Luxembourg_20200327_null_1":"background",
"epi_isl_429845_Iowa_20200414_null_1":"background",
"epi_isl_429990_California_20200321_null_1":"background",
"epi_isl_430137_Washington_20200321_null_1":"background",
"epi_isl_430628_Victoria_20200411_null_2":"background",
"epi_isl_430715_Victoria_20200417_null_1":"background",
"epi_isl_430896_Washington_20200329_null_1":"background",
"epi_isl_432041_Wales_20200401_null_1":"background",
"epi_isl_432044_Wales_20200408_null_1":"background",
"epi_isl_432420_Wales_20200330_null_2":"background",
"epi_isl_432607_England_20200404_null_1":"background",
"epi_isl_432900_England_20200302_null_2":"background",
"epi_isl_433307_Scotland_20200324_null_1":"background",
"epi_isl_433953_England_20200413_null_1":"background",
"epi_isl_435144_Madrid_20200311_null_1":"background",
"epi_isl_435402_Iowa_20200426_null_1":"background",
"epi_isl_435415_Baranya_20200330_null_1":"background",
"epi_isl_435634_California_20200310_null_1":"background",
"epi_isl_435686_Singapore_20200413_null_2":"background",
"epi_isl_436118_Victoria_20200411_null_10":"background",
"epi_isl_436418_Tamil_Nadu_20200331_null_2":"background",
"epi_isl_436517_Florida_20200408_null_1":"background",
"epi_isl_436725_Abruzzo_20200427_null_1":"background",
"epi_isl_437074_California_20200421_null_1":"background",
"epi_isl_437154_Michigan_20200322_null_2":"background",
"epi_isl_437301_Styria_20200417_null_2":"background",
"epi_isl_437384_Minnesota_20200416_null_8":"background",
"epi_isl_437476_Makkah_20200409_null_1":"background",
"epi_isl_437478_Makkah_20200409_null_1":"background",
"epi_isl_437636_Unknown_20200331_null_2":"background",
"epi_isl_437860_Washington_20200404_null_17":"background",
"epi_isl_437867_Connecticut_20200402_null_1":"background",
"epi_isl_438106_Vienna_20200325_null_6":"background",
"epi_isl_438536_England_20200401_null_2":"background",
"epi_isl_438844_Scotland_20200405_null_2":"background",
"epi_isl_439249_Scotland_20200426_null_3":"background",
"epi_isl_439286_Scotland_20200414_null_5":"background",
"epi_isl_439341_Scotland_20200430_null_1":"background",
"epi_isl_439507_England_20200330_null_1":"background",
"epi_isl_439984_England_20200320_null_5":"background",
"epi_isl_440124_England_20200321_null_1":"background",
"epi_isl_440219_England_20200309_null_2":"background",
"epi_isl_440525_England_20200310_null_2":"background",
"epi_isl_440875_England_20200423_null_4":"background",
"epi_isl_441112_England_20200331_null_4":"background",
"epi_isl_441633_England_20200407_null_1":"background",
"epi_isl_441767_England_20200407_null_12":"background",
"epi_isl_442014_England_20200409_null_1":"background",
"epi_isl_442155_England_20200404_null_1":"background",
"epi_isl_442776_England_20200406_null_3":"background",
"epi_isl_442896_England_20200408_null_7":"background",
"epi_isl_442980_England_20200412_null_12":"background",
"epi_isl_443051_England_20200412_null_3":"background",
"epi_isl_443092_England_20200407_null_25":"background",
"epi_isl_443306_Ile_de_France_20200402_null_1":"background",
"epi_isl_443368_England_20200416_null_2":"background",
"epi_isl_443458_England_20200414_null_9":"background",
"epi_isl_443634_England_20200413_null_1":"background",
"epi_isl_443761_England_20200325_null_1":"background",
"epi_isl_444068_California_20200430_null_2":"background",
"epi_isl_444156_England_20200413_null_4":"background",
"epi_isl_444259_England_20200419_null_6":"background",
"epi_isl_445040_Florida_20200428_null_3":"background",
"epi_isl_445136_Louisiana_20200331_null_22391":"background"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":3
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":7
}
}
}