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[0.000306066224397489, 0.001099648503973805, 0, 0, 0.2177299691183482, 0, 0, 0, 1, 1, 3518.868085350784],
[0.0004169686023205378, 0.0009600873256431151, 0, 0, 0.3027971441487768, 0, 0, 0, 1, 1, 3518.868085350784],
[0.0005900954280003018, 0.0006760581220403021, 0, 0, 0.4660536062007473, 0, 0, 0, 1, 1, 3518.868085350784],
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]
}
}
},
"headers": [
["ES", "Expected synonymous sites"],
["EN", "Expected non-synonymous sites"],
["S", "Inferred synonymous substitutions"],
["N", "Inferred non-synonymous substitutions"],
["P[S]", "Expected proportion of synonymous sites"],
["dS", "Inferred synonymous susbsitution rate"],
["dN", "Inferred non-synonymous susbsitution rate"],
["dN-dS", "Scaled by the length of the tested branches"],
["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"],
["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
]
},
"analysis":{
"authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
"citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
"contact":"spond@temple.edu",
"info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.00"
},
"branch attributes":{
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],
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
"amino-acid": [
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"Global MG94xREV":0.006907596162513728,
"Nucleotide GTR":0.008786902999351094,
"amino-acid": [
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"Global MG94xREV":0.006912785649293697,
"Nucleotide GTR":0.008793504357606433,
"amino-acid": [
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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", "VL", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-"]
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"original name":"epi_isl_423904_England_20200318_null_1",
"synonymous substitution count": [
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"epi_isl_424158_England_20200321_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_424158_England_20200321_null_1",
"synonymous substitution count": [
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]
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"epi_isl_424288_Washington_20200322_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "V", "K", "L", "I", "L", "V", "V", "L", "S", "P", "C", "-", "-", "-", "-", "-"]
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"codon": [
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"synonymous substitution count": [
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]
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"epi_isl_424315_Idaho_20200320_null_1":{
"Global MG94xREV":0.2534858635939822,
"Nucleotide GTR":0.3224501900088658,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_424315_Idaho_20200320_null_1",
"synonymous substitution count": [
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]
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"epi_isl_424366_Kayseri_20200317_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_424366_Kayseri_20200317_null_3",
"synonymous substitution count": [
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]
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"epi_isl_424479_Reykjavik_20200320_null_1":{
"Global MG94xREV":0.7991738763418047,
"Nucleotide GTR":1.01660015522323,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_424479_Reykjavik_20200320_null_1",
"synonymous substitution count": [
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]
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"epi_isl_424600_Reykjavik_20200327_null_1":{
"Global MG94xREV":0.006908608710192094,
"Nucleotide GTR":0.008788191024594995,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_424600_Reykjavik_20200327_null_1",
"synonymous substitution count": [
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"epi_isl_425251_England_20200331_null_1":{
"Global MG94xREV":0.006911994040862294,
"Nucleotide GTR":0.008792497381179829,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_425251_England_20200331_null_1",
"synonymous substitution count": [
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"epi_isl_426103_Washington_20200323_null_2":{
"Global MG94xREV":0.3057675142783962,
"Nucleotide GTR":0.3889557850670927,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_426103_Washington_20200323_null_2",
"synonymous substitution count": [
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},
"epi_isl_426899_Northern_territory_20200327_null_2":{
"Global MG94xREV":0.006949439181555889,
"Nucleotide GTR":0.008840129989011942,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_426899_Northern_territory_20200327_null_2",
"synonymous substitution count": [
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"epi_isl_426949_Victoria_20200328_null_1":{
"Global MG94xREV":0.006954608882179543,
"Nucleotide GTR":0.008846706178014162,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_426949_Victoria_20200328_null_1",
"synonymous substitution count": [
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"epi_isl_427272_Arizona_20200323_null_3":{
"Global MG94xREV":0.02114681505910661,
"Nucleotide GTR":0.02690009784850642,
"amino-acid": [
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"Nucleotide GTR":1.454729148090535,
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"Nucleotide GTR":0.008794662570677183,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.00884688606539575,
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"epi_isl_430903_USA_20200405_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":0,
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"epi_isl_432289_Wales_20200401_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":0.009005954503498078,
"amino-acid": [
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"codon": [
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_433319_Scotland_20200325_null_1":{
"Global MG94xREV":0.0069518468692111,
"Nucleotide GTR":0.00884319272131147,
"amino-acid": [
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"epi_isl_433486_England_20200417_null_1":{
"Global MG94xREV":0.006950397688396072,
"Nucleotide GTR":0.008841349270862062,
"amino-acid": [
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"epi_isl_433657_Scotland_20200405_null_1":{
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"Nucleotide GTR":0.008849856547653804,
"amino-acid": [
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"original name":"epi_isl_433657_Scotland_20200405_null_1",
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"epi_isl_433714_England_20200405_null_1":{
"Global MG94xREV":0.007074622168237642,
"Nucleotide GTR":0.00899937073431073,
"amino-acid": [
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"original name":"epi_isl_433714_England_20200405_null_1",
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]
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"epi_isl_434251_Washington_20200402_null_1":{
"Global MG94xREV":0.006956407727387515,
"Nucleotide GTR":0.008848994423878792,
"amino-acid": [
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"original name":"epi_isl_434251_Washington_20200402_null_1",
"synonymous substitution count": [
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"epi_isl_434332_Washington_20200326_null_1":{
"Global MG94xREV":0.006913106458663001,
"Nucleotide GTR":0.008793912447590719,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_434332_Washington_20200326_null_1",
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]
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"epi_isl_435058_KZN_20200311_null_1":{
"Global MG94xREV":0.007095409017415708,
"Nucleotide GTR":0.00902581293259396,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_435058_KZN_20200311_null_1",
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]
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"epi_isl_435600_California_20200305_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_435600_California_20200305_null_3",
"synonymous substitution count": [
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]
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"epi_isl_437478_Makkah_20200409_null_1":{
"Global MG94xREV":0.2351428518308699,
"Nucleotide GTR":0.2991167088257721,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_437478_Makkah_20200409_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_437867_Connecticut_20200402_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_437867_Connecticut_20200402_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_437869_Connecticut_20200403_null_11":{
"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_437869_Connecticut_20200403_null_11",
"synonymous substitution count": [
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]
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"epi_isl_438253_England_20200404_null_2":{
"Global MG94xREV":0.006914079477101941,
"Nucleotide GTR":0.008795150189120237,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_438253_England_20200404_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_438401_England_20200329_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_438401_England_20200329_null_1",
"synonymous substitution count": [
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"epi_isl_438801_Scotland_20200401_null_19":{
"Global MG94xREV":0.006947305231315802,
"Nucleotide GTR":0.008837415468167929,
"amino-acid": [
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"original name":"epi_isl_438801_Scotland_20200401_null_19",
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]
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"epi_isl_438977_Scotland_20200420_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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],
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"original name":"epi_isl_438977_Scotland_20200420_null_1",
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]
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"epi_isl_438995_Scotland_20200422_null_2":{
"Global MG94xREV":0.006951023544231057,
"Nucleotide GTR":0.008842145399411593,
"amino-acid": [
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],
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"original name":"epi_isl_438995_Scotland_20200422_null_2",
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]
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"epi_isl_439881_England_20200323_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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],
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"original name":"epi_isl_439881_England_20200323_null_1",
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]
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"epi_isl_440074_England_20200323_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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],
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"original name":"epi_isl_440074_England_20200323_null_3",
"synonymous substitution count": [
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]
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"epi_isl_440493_England_20200310_null_4":{
"Global MG94xREV":0.006949572208654837,
"Nucleotide GTR":0.008840299207968468,
"amino-acid": [
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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":{
"Global MG94xREV":0.006909003737098802,
"Nucleotide GTR":0.008788693524021672,
"amino-acid": [
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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_440887_England_20200418_null_1":{
"Global MG94xREV":0.0069140296199976,
"Nucleotide GTR":0.00879508676770281,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_440887_England_20200418_null_1",
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]
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"epi_isl_441602_England_20200406_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_441602_England_20200406_null_1",
"synonymous substitution count": [
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"epi_isl_442012_England_20200324_null_3":{
"Global MG94xREV":0.00694841700898887,
"Nucleotide GTR":0.008838829720295635,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_442012_England_20200324_null_3",
"synonymous substitution count": [
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]
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"epi_isl_442129_England_20200407_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_442129_England_20200407_null_1",
"synonymous substitution count": [
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]
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"epi_isl_442145_England_20200405_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_442145_England_20200405_null_1",
"synonymous substitution count": [
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]
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"epi_isl_442883_England_20200410_null_1":{
"Global MG94xREV":0.006913787214056804,
"Nucleotide GTR":0.008794778411881464,
"amino-acid": [
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"codon": [
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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":0.006934152778753806,
"Nucleotide GTR":0.008820684709428303,
"amino-acid": [
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"codon": [
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 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_443363_England_20200414_null_2",
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]
},
"epi_isl_443483_England_20200413_null_31":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_443483_England_20200413_null_31",
"synonymous substitution count": [
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]
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"epi_isl_443597_England_20200414_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-"]
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"codon": [
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],
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"original name":"epi_isl_443597_England_20200414_null_1",
"synonymous substitution count": [
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]
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"epi_isl_443691_England_20200330_null_2":{
"Global MG94xREV":0.006957095516716329,
"Nucleotide GTR":0.008849869335783597,
"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", "H", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-"]
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"codon": [
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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"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": [
["IM", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-"]
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"codon": [
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],
"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_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":0.001336758456130741,
"Nucleotide GTR":0.001700442036743024,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444149_England_20200409_null_4",
"synonymous substitution count": [
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]
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"epi_isl_444355_England_20200101_null_29":{
"Global MG94xREV":0.001384383145797554,
"Nucleotide GTR":0.00176102368028893,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444355_England_20200101_null_29",
"synonymous substitution count": [
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]
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"epi_isl_444437_England_20200418_null_23":{
"Global MG94xREV":0.002601534700841312,
"Nucleotide GTR":0.003309318108344618,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444437_England_20200418_null_23",
"synonymous substitution count": [
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]
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"epi_isl_444604_Illinois_20200321_null_18":{
"Global MG94xREV":0.006916791752176428,
"Nucleotide GTR":0.00879860037604871,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444604_Illinois_20200321_null_18",
"synonymous substitution count": [
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]
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"epi_isl_444822_Unknown_20200311_null_6":{
"Global MG94xREV":0.0008758475652890481,
"Nucleotide GTR":0.001114133979079063,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444822_Unknown_20200311_null_6",
"synonymous substitution count": [
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]
},
"epi_isl_444995_South_Carolina_20200327_null_17":{
"Global MG94xREV":0.006947480906922934,
"Nucleotide GTR":0.008837638938747719,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_444995_South_Carolina_20200327_null_17",
"synonymous substitution count": [
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]
},
"epi_isl_445873_Wales_20200408_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_445873_Wales_20200408_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_446256_Wales_20200417_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["ML", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "-", "T", "I", "Y", "S", "L", "L", "L", "C", "R", "M", "N", "S", "R", "N", "Y", "I", "A", "Q", "V", "D", "V", "V", "N", "F", "N", "L", "T", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_446256_Wales_20200417_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_446888_Wales_20200417_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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"nonsynonymous substitution count": [
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],
"original name":"epi_isl_446888_Wales_20200417_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_446927_Wales_20200417_null_17":{
"Global MG94xREV":0.006913530317345596,
"Nucleotide GTR":0.008794451622875692,
"amino-acid": [
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"original name":"epi_isl_446927_Wales_20200417_null_17",
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"epi_isl_447015_Bangkok_20200331_null_6":{
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"Nucleotide GTR":0,
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"original name":"epi_isl_447015_Bangkok_20200331_null_6",
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"epi_isl_447423_Jerusalem_District_20200404_null_16":{
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"Nucleotide GTR":0.001861669189244074,
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"nonsynonymous substitution count": [
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"original name":"epi_isl_447423_Jerusalem_District_20200404_null_16",
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"Nucleotide GTR":0.008837782628781793,
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"original name":"epi_isl_447494_Comunitat_Valenciana_20200326_null_13",
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"Nucleotide GTR":0.008841379767752677,
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"original name":"epi_isl_447517_Comunitat_Valenciana_20200401_null_3",
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"epi_isl_447596_Kinshasa_20200405_null_10":{
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"Nucleotide GTR":0.003077206601116424,
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"codon": [
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"original name":"epi_isl_447596_Kinshasa_20200405_null_10",
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"epi_isl_447617_Taipei_20200325_null_4":{
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"Nucleotide GTR":0.008841475107858961,
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"codon": [
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"epi_isl_447795_Valle_del_Cauca_20200404_null_25725":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_447803_Meta_20200404_null_310":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_447803_Meta_20200404_null_310",
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]
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"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":{
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},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
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}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
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"Equilibrium frequencies": [
[0.03082070114327564],
[0.02318190691744819],
[0.01441572613542214],
[0.03652529975082406],
[0.01623968181649858],
[0.01221473809077125],
[0.007595765083498592],
[0.01924548190672914],
[0.01503439433388932],
[0.01130817655277362],
[0.007032017549561054],
[0.01781710795820772],
[0.04545896613745652],
[0.03419213328934493],
[0.02126246262830327],
[0.05387295885367687],
[0.01330827540385191],
[0.01000986967200031],
[0.006224662205602046],
[0.01577150195359081],
[0.007012240152493806],
[0.005274282948406263],
[0.003279825892481885],
[0.00831013455222711],
[0.006491801059145048],
[0.004882832716235141],
[0.003036401597719533],
[0.007693367470964332],
[0.01962902914243541],
[0.01476404849923715],
[0.009181060064342685],
[0.02326216298299682],
[0.0177042604914951],
[0.01331632647966669],
[0.008280790546883795],
[0.02098113921264945],
[0.009328520978213224],
[0.00701648233079159],
[0.004363216886122071],
[0.0110551354226874],
[0.008636170617328968],
[0.006495728388638583],
[0.004039384759595459],
[0.01023463804508618],
[0.02611288349444891],
[0.01964090406965178],
[0.01221374475915484],
[0.03094611289208731],
[0.02010096826462994],
[0.03167098779931727],
[0.01408138381296972],
[0.01059136608552936],
[0.006586267188143651],
[0.01668770487355817],
[0.009805289048376358],
[0.006097443238962288],
[0.01544916571836715],
[0.0394173455585804],
[0.02964790552376073],
[0.01843662335636928],
[0.0467130956955234]
],
"Log Likelihood":-inf,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *background*": [
[0.9165418920175951, 1]
],
"non-synonymous/synonymous rate ratio for *test*": [
[0.9165418920175951, 1]
]
},
"display order":1,
"estimated parameters":131
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"Nucleotide GTR":{
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"Equilibrium frequencies": [
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[0.1831628113879004],
[0.1588078291814947],
[0.3587077402135231]
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"Log Likelihood":-774.1888171430076,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.4058124085366741,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.09831637126336258,
"Substitution rate from nucleotide C to nucleotide G":0.223944970781064,
"Substitution rate from nucleotide C to nucleotide T":1.428822751203306,
"Substitution rate from nucleotide G to nucleotide T":0.7514376827216609
},
"display order":0,
"estimated parameters":193
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-18/sequences.ORF10.compressed.fas",
"number of sequences":94,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_433486_England_20200417_null_1,epi_isl_442883_England_20200410_null_1,epi_isl_426899_Northern_territory_20200327_null_2,epi_isl_432401_Wales_20200330_null_1,epi_isl_440887_England_20200418_null_1,(epi_isl_443363_England_20200414_null_2,epi_isl_446888_Wales_20200417_null_1)Node140,epi_isl_423536_England_20200331_null_1,epi_isl_441602_England_20200406_null_1,(epi_isl_437478_Makkah_20200409_null_1,epi_isl_437867_Connecticut_20200402_null_1)Node134,epi_isl_438977_Scotland_20200420_null_1,epi_isl_447617_Taipei_20200325_null_4,epi_isl_430709_Victoria_20200407_null_1,epi_isl_443691_England_20200330_null_2,epi_isl_430520_Victoria_20200402_null_1,epi_isl_446927_Wales_20200417_null_17,(epi_isl_423904_England_20200318_null_1,epi_isl_444822_Unknown_20200311_null_6)Node157,(epi_isl_442129_England_20200407_null_1,epi_isl_447596_Kinshasa_20200405_null_10)Node160,epi_isl_442012_England_20200324_null_3,epi_isl_430566_Victoria_20200406_null_1,epi_isl_424600_Reykjavik_20200327_null_1,epi_isl_433714_England_20200405_null_1,epi_isl_429464_Unknown_20200323_null_1,epi_isl_422051_Wales_20200330_null_1,epi_isl_430737_Beijing_20200225_null_5,epi_isl_427272_Arizona_20200323_null_3,epi_isl_446256_Wales_20200417_null_2,(epi_isl_426103_Washington_20200323_null_2,epi_isl_430896_Washington_20200329_null_1)Node173,epi_isl_444065_California_20200430_null_1,epi_isl_422206_Wales_20200330_null_1,epi_isl_433657_Scotland_20200405_null_1,epi_isl_407073_England_20200129_null_1,epi_isl_414480_USA_20200221_null_1,(epi_isl_438401_England_20200329_null_1,epi_isl_444355_England_20200101_null_29)Node117,(epi_isl_430608_Victoria_20200408_null_1,epi_isl_447423_Jerusalem_District_20200404_null_16)Node114,epi_isl_417222_England_20200304_null_1,epi_isl_432289_Wales_20200401_null_1,epi_isl_447803_Meta_20200404_null_310,epi_isl_440074_England_20200323_null_3,epi_isl_432226_Wales_20200404_null_1,epi_isl_434332_Washington_20200326_null_1,epi_isl_439881_England_20200323_null_1,epi_isl_447494_Comunitat_Valenciana_20200326_null_13,((((epi_isl_430903_USA_20200405_null_3,epi_isl_424288_Washington_20200322_null_1,epi_isl_428685_Madrid_20200327_null_1)Node69,epi_isl_415435_Wales_20200306_null_1)Node68,(((epi_isl_422425_Zhejiang_20200124_null_1,epi_isl_424315_Idaho_20200320_null_1)Node78,epi_isl_418999_Singapore_20200301_null_4)Node77,epi_isl_429689_Minas_gerais_20200317_null_1)Node76,epi_isl_437869_Connecticut_20200403_null_11)Node67,epi_isl_447015_Bangkok_20200331_null_6)Node66,epi_isl_426949_Victoria_20200328_null_1,epi_isl_425251_England_20200331_null_1,epi_isl_447517_Comunitat_Valenciana_20200401_null_3,epi_isl_416677_Washington_20200312_null_1,epi_isl_440493_England_20200310_null_4,(epi_isl_421889_England_20200327_null_1,epi_isl_444437_England_20200418_null_23)Node34,epi_isl_445873_Wales_20200408_null_2,((epi_isl_422636_Prague_20200308_null_1,epi_isl_422985_Washington_20200317_null_1)Node40,epi_isl_443483_England_20200413_null_31)Node39,epi_isl_434251_Washington_20200402_null_1,epi_isl_447795_Valle_del_Cauca_20200404_null_25725,epi_isl_438253_England_20200404_null_2,epi_isl_435058_KZN_20200311_null_1,epi_isl_423770_England_20200322_null_1,epi_isl_433319_Scotland_20200325_null_1,epi_isl_444995_South_Carolina_20200327_null_17,epi_isl_435600_California_20200305_null_3,epi_isl_443597_England_20200414_null_1,(epi_isl_414937_Shandong_20200126_null_1,epi_isl_432653_England_20200318_null_1)Node17,epi_isl_424158_England_20200321_null_1,(epi_isl_442145_England_20200405_null_1,epi_isl_444149_England_20200409_null_4)Node111,epi_isl_438995_Scotland_20200422_null_2,epi_isl_440730_England_20200402_null_1,epi_isl_444604_Illinois_20200321_null_18,epi_isl_414934_Shandong_20200121_null_1,((epi_isl_416604_unknown_20200216_null_1,epi_isl_418182_Madrid_20200312_null_3,epi_isl_416567_unknown_20200215_null_1,epi_isl_424479_Reykjavik_20200320_null_1)Node97,epi_isl_424366_Kayseri_20200317_null_3)Node96,epi_isl_438801_Scotland_20200401_null_19)"
}
},
"tested":{
"0":{
"Node111":"test",
"Node114":"test",
"Node117":"test",
"Node134":"test",
"Node140":"test",
"Node157":"test",
"Node160":"test",
"Node17":"test",
"Node173":"test",
"Node34":"test",
"Node39":"test",
"Node40":"test",
"Node66":"test",
"Node67":"test",
"Node68":"test",
"Node69":"test",
"Node76":"test",
"Node77":"test",
"Node78":"test",
"Node96":"test",
"Node97":"test",
"epi_isl_407073_England_20200129_null_1":"background",
"epi_isl_414480_USA_20200221_null_1":"background",
"epi_isl_414934_Shandong_20200121_null_1":"background",
"epi_isl_414937_Shandong_20200126_null_1":"background",
"epi_isl_415435_Wales_20200306_null_1":"background",
"epi_isl_416567_unknown_20200215_null_1":"background",
"epi_isl_416604_unknown_20200216_null_1":"background",
"epi_isl_416677_Washington_20200312_null_1":"background",
"epi_isl_417222_England_20200304_null_1":"background",
"epi_isl_418182_Madrid_20200312_null_3":"background",
"epi_isl_418999_Singapore_20200301_null_4":"background",
"epi_isl_421889_England_20200327_null_1":"background",
"epi_isl_422051_Wales_20200330_null_1":"background",
"epi_isl_422206_Wales_20200330_null_1":"background",
"epi_isl_422425_Zhejiang_20200124_null_1":"background",
"epi_isl_422636_Prague_20200308_null_1":"background",
"epi_isl_422985_Washington_20200317_null_1":"background",
"epi_isl_423536_England_20200331_null_1":"background",
"epi_isl_423770_England_20200322_null_1":"background",
"epi_isl_423904_England_20200318_null_1":"background",
"epi_isl_424158_England_20200321_null_1":"background",
"epi_isl_424288_Washington_20200322_null_1":"background",
"epi_isl_424315_Idaho_20200320_null_1":"background",
"epi_isl_424366_Kayseri_20200317_null_3":"background",
"epi_isl_424479_Reykjavik_20200320_null_1":"background",
"epi_isl_424600_Reykjavik_20200327_null_1":"background",
"epi_isl_425251_England_20200331_null_1":"background",
"epi_isl_426103_Washington_20200323_null_2":"background",
"epi_isl_426899_Northern_territory_20200327_null_2":"background",
"epi_isl_426949_Victoria_20200328_null_1":"background",
"epi_isl_427272_Arizona_20200323_null_3":"background",
"epi_isl_428685_Madrid_20200327_null_1":"background",
"epi_isl_429464_Unknown_20200323_null_1":"background",
"epi_isl_429689_Minas_gerais_20200317_null_1":"background",
"epi_isl_430520_Victoria_20200402_null_1":"background",
"epi_isl_430566_Victoria_20200406_null_1":"background",
"epi_isl_430608_Victoria_20200408_null_1":"background",
"epi_isl_430709_Victoria_20200407_null_1":"background",
"epi_isl_430737_Beijing_20200225_null_5":"background",
"epi_isl_430896_Washington_20200329_null_1":"background",
"epi_isl_430903_USA_20200405_null_3":"background",
"epi_isl_432226_Wales_20200404_null_1":"background",
"epi_isl_432289_Wales_20200401_null_1":"background",
"epi_isl_432401_Wales_20200330_null_1":"background",
"epi_isl_432653_England_20200318_null_1":"background",
"epi_isl_433319_Scotland_20200325_null_1":"background",
"epi_isl_433486_England_20200417_null_1":"background",
"epi_isl_433657_Scotland_20200405_null_1":"background",
"epi_isl_433714_England_20200405_null_1":"background",
"epi_isl_434251_Washington_20200402_null_1":"background",
"epi_isl_434332_Washington_20200326_null_1":"background",
"epi_isl_435058_KZN_20200311_null_1":"background",
"epi_isl_435600_California_20200305_null_3":"background",
"epi_isl_437478_Makkah_20200409_null_1":"background",
"epi_isl_437867_Connecticut_20200402_null_1":"background",
"epi_isl_437869_Connecticut_20200403_null_11":"background",
"epi_isl_438253_England_20200404_null_2":"background",
"epi_isl_438401_England_20200329_null_1":"background",
"epi_isl_438801_Scotland_20200401_null_19":"background",
"epi_isl_438977_Scotland_20200420_null_1":"background",
"epi_isl_438995_Scotland_20200422_null_2":"background",
"epi_isl_439881_England_20200323_null_1":"background",
"epi_isl_440074_England_20200323_null_3":"background",
"epi_isl_440493_England_20200310_null_4":"background",
"epi_isl_440730_England_20200402_null_1":"background",
"epi_isl_440887_England_20200418_null_1":"background",
"epi_isl_441602_England_20200406_null_1":"background",
"epi_isl_442012_England_20200324_null_3":"background",
"epi_isl_442129_England_20200407_null_1":"background",
"epi_isl_442145_England_20200405_null_1":"background",
"epi_isl_442883_England_20200410_null_1":"background",
"epi_isl_443363_England_20200414_null_2":"background",
"epi_isl_443483_England_20200413_null_31":"background",
"epi_isl_443597_England_20200414_null_1":"background",
"epi_isl_443691_England_20200330_null_2":"background",
"epi_isl_444065_California_20200430_null_1":"background",
"epi_isl_444149_England_20200409_null_4":"background",
"epi_isl_444355_England_20200101_null_29":"background",
"epi_isl_444437_England_20200418_null_23":"background",
"epi_isl_444604_Illinois_20200321_null_18":"background",
"epi_isl_444822_Unknown_20200311_null_6":"background",
"epi_isl_444995_South_Carolina_20200327_null_17":"background",
"epi_isl_445873_Wales_20200408_null_2":"background",
"epi_isl_446256_Wales_20200417_null_2":"background",
"epi_isl_446888_Wales_20200417_null_1":"background",
"epi_isl_446927_Wales_20200417_null_17":"background",
"epi_isl_447015_Bangkok_20200331_null_6":"background",
"epi_isl_447423_Jerusalem_District_20200404_null_16":"background",
"epi_isl_447494_Comunitat_Valenciana_20200326_null_13":"background",
"epi_isl_447517_Comunitat_Valenciana_20200401_null_3":"background",
"epi_isl_447596_Kinshasa_20200405_null_10":"background",
"epi_isl_447617_Taipei_20200325_null_4":"background",
"epi_isl_447795_Valle_del_Cauca_20200404_null_25725":"background",
"epi_isl_447803_Meta_20200404_null_310":"background"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}