{
"MLE":{
"content":{
"0":{
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],
"NAMES": [
["epi_isl_433971_England_20200413_null_2"],
["epi_isl_431963_Wales_20200330_null_3"],
["epi_isl_434971_Texas_20200331_null_6"],
["epi_isl_430342_New_York_20200330_null_1"],
["epi_isl_430363_New_York_20200408_null_2"],
["epi_isl_435019_Texas_20200402_null_11"],
["epi_isl_424582_Reykjavik_20200327_null_1"],
["epi_isl_430388_New_York_20200409_null_7"],
["Node58"],
["epi_isl_421487_Portugal_20200322_null_1"],
["epi_isl_435455_Louisiana_20200402_null_1"],
["epi_isl_427377_Liege_20200407_null_2"],
["epi_isl_419839_Victoria_20200316_null_1"],
["epi_isl_430926_Connecticut_20200404_null_1"],
["epi_isl_432224_Wales_20200331_null_1"],
["epi_isl_427473_New_York_20200401_null_1"],
["epi_isl_430225_Washington_20200320_null_2"],
["epi_isl_430429_New_York_20200413_null_2"],
["epi_isl_433289_Scotland_20200323_null_2"],
["epi_isl_435389_Utah_20200406_null_28"],
["epi_isl_421660_Ohio_20200401_null_1"],
["epi_isl_430415_New_York_20200410_null_1"],
["epi_isl_435412_Baranya_20200330_null_5"],
["epi_isl_429644_Washington_20200408_null_4"],
["epi_isl_424597_Reykjavik_20200327_null_2"],
["epi_isl_432537_England_20200320_null_1"],
["epi_isl_433553_Scotland_20200401_null_1"],
["epi_isl_424545_Reykjavik_20200325_null_2"],
["epi_isl_427041_Victoria_20200329_null_1"],
["epi_isl_432861_England_20200401_null_1"],
["epi_isl_424503_Reykjavik_20200320_null_1"],
["epi_isl_433922_England_20200411_null_1"],
["epi_isl_434383_Antwerp_20200410_null_1"],
["Node112"],
["epi_isl_435457_Louisiana_20200402_null_3"],
["epi_isl_418972_New_York_20200317_null_1"],
["epi_isl_422283_Wales_20200327_null_2"],
["epi_isl_419186_ARA_20200322_null_4"],
["epi_isl_430668_Victoria_20200403_null_2"],
["epi_isl_433621_Scotland_20200404_null_1"],
["epi_isl_421955_England_20200330_null_1"],
["epi_isl_434172_Washington_20200330_null_16"],
["epi_isl_434030_England_20200414_null_2"],
["epi_isl_435578_Louisiana_20200424_null_4"],
["epi_isl_424355_Beijing_20200124_null_1"],
["epi_isl_423486_England_20200331_null_4"],
["epi_isl_428787_New_York_20200406_null_1"],
["epi_isl_422654_Netherlands_20200318_null_1"],
["epi_isl_417445_Lombardy_20200224_null_1"],
["epi_isl_406799_Wuhan_20191231_null_1"],
["epi_isl_418031_Washington_20200316_null_1"],
["Node16"],
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["Node15"],
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["epi_isl_429678_Minas_gerais_20200316_null_7"],
["epi_isl_430362_New_York_20200408_null_2"],
["Node28"],
["epi_isl_420300_New_York_20200318_null_1"],
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["Node24"],
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["epi_isl_422544_New_York_20200320_null_1"],
["epi_isl_435642_California_20200312_null_1"],
["epi_isl_435671_California_20200321_null_15701"],
["epi_isl_429534_Unknown_20200325_null_1"],
["epi_isl_426102_Washington_20200325_null_3"],
["epi_isl_432546_England_20200321_null_3"],
["epi_isl_432731_England_20200402_null_3"]
],
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[0.001377722332471257, 0.0029240700122597, 1, 0, 0.3202670473294132, 725.8356610989048, 0, -1.376330403599159, 1, 0.3202670473294132, 527.3702151756696]
]
}
}
},
"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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"Nucleotide GTR":0.008180219496617047,
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"Nucleotide GTR":516.2278849561651,
"amino-acid": [
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"Nucleotide GTR":0.004027259495208414,
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"Nucleotide GTR":0.004020185979078562,
"amino-acid": [
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"Nucleotide GTR":0.004023665700816433,
"amino-acid": [
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"Nucleotide GTR":0.004033420798303579,
"amino-acid": [
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"Nucleotide GTR":0.004028179533035964,
"amino-acid": [
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"synonymous substitution count": [
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"epi_isl_421660_Ohio_20200401_null_1":{
"Global MG94xREV":0.004118610847187742,
"Nucleotide GTR":0.004037246420094129,
"amino-acid": [
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"codon": [
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]
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"Nucleotide GTR":0,
"amino-acid": [
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"Global MG94xREV":0.004108422799552431,
"Nucleotide GTR":0.004027259640480927,
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"original name":"epi_isl_421955_England_20200330_null_1",
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"Global MG94xREV":0.004102722432649108,
"Nucleotide GTR":0.004021671886083259,
"amino-acid": [
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],
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"original name":"epi_isl_422283_Wales_20200327_null_2",
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"epi_isl_422544_New_York_20200320_null_1":{
"Global MG94xREV":0.004102759658743381,
"Nucleotide GTR":0.004021708376764559,
"amino-acid": [
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]
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"epi_isl_422654_Netherlands_20200318_null_1":{
"Global MG94xREV":0.004120499121561121,
"Nucleotide GTR":0.004039097391025087,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_422654_Netherlands_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_423486_England_20200331_null_4":{
"Global MG94xREV":0.004102682456886886,
"Nucleotide GTR":0.004021632700054537,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_423486_England_20200331_null_4",
"synonymous substitution count": [
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]
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"epi_isl_424355_Beijing_20200124_null_1":{
"Global MG94xREV":0.004109301293810549,
"Nucleotide GTR":0.004028120779814125,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_424355_Beijing_20200124_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_424503_Reykjavik_20200320_null_1":{
"Global MG94xREV":0.004102624364673072,
"Nucleotide GTR":0.004021575755470327,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_424503_Reykjavik_20200320_null_1",
"synonymous substitution count": [
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]
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"Nucleotide GTR":0.004021651576718401,
"amino-acid": [
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"Global MG94xREV":0.004115375623039459,
"Nucleotide GTR":0.004034075108796344,
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"original name":"epi_isl_424582_Reykjavik_20200327_null_1",
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"Global MG94xREV":0.004108334068728586,
"Nucleotide GTR":0.00402717266256186,
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"original name":"epi_isl_424597_Reykjavik_20200327_null_2",
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"Global MG94xREV":0.004108520411425356,
"Nucleotide GTR":0.004027355324001209,
"amino-acid": [
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"original name":"epi_isl_426102_Washington_20200325_null_3",
"synonymous substitution count": [
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"epi_isl_426880_Victoria_20200323_null_2":{
"Global MG94xREV":0.004105124353454372,
"Nucleotide GTR":0.004024026356202474,
"amino-acid": [
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],
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"original name":"epi_isl_426880_Victoria_20200323_null_2",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.004155891685967587,
"Nucleotide GTR":0.004073790764409835,
"amino-acid": [
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],
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],
"original name":"epi_isl_427041_Victoria_20200329_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_427377_Liege_20200407_null_2":{
"Global MG94xREV":0.004102722428573316,
"Nucleotide GTR":0.004021671882087982,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_427377_Liege_20200407_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_427473_New_York_20200401_null_1":{
"Global MG94xREV":0.004109393734653547,
"Nucleotide GTR":0.004028211394459772,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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"Nucleotide GTR":0.00402842560311138,
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"Nucleotide GTR":0.00402157871274986,
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"Nucleotide GTR":0.004028211396805224,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.004023605945631201,
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"Nucleotide GTR":0.004023605838832431,
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"Nucleotide GTR":0.00403374649355623,
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"Nucleotide GTR":0.004027622431543589,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.004028444531020248,
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"Nucleotide GTR":0.004027603325082301,
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"Nucleotide GTR":0.004027526706077112,
"amino-acid": [
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"Nucleotide GTR":0.00402187813372898,
"amino-acid": [
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"Nucleotide GTR":0.004027259639349694,
"amino-acid": [
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"original name":"epi_isl_431963_Wales_20200330_null_3",
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"epi_isl_432224_Wales_20200331_null_1":{
"Global MG94xREV":0.004108422797232783,
"Nucleotide GTR":0.004027259638207103,
"amino-acid": [
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],
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],
"original name":"epi_isl_432224_Wales_20200331_null_1",
"synonymous substitution count": [
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"epi_isl_432537_England_20200320_null_1":{
"Global MG94xREV":0.004102952461583471,
"Nucleotide GTR":0.004021897370725096,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
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]
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"Global MG94xREV":0.004104675410420478,
"Nucleotide GTR":0.004023586282176634,
"amino-acid": [
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"Global MG94xREV":0.00410881240427145,
"Nucleotide GTR":0.004027641548438602,
"amino-acid": [
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"Global MG94xREV":0.004108753846069235,
"Nucleotide GTR":0.004027584147071726,
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"epi_isl_433206_Scotland_20200402_null_2":{
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"Nucleotide GTR":0,
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],
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"original name":"epi_isl_433206_Scotland_20200402_null_2",
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"epi_isl_433289_Scotland_20200323_null_2":{
"Global MG94xREV":0.004102627381462121,
"Nucleotide GTR":0.00402157871266177,
"amino-acid": [
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],
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],
"original name":"epi_isl_433289_Scotland_20200323_null_2",
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]
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"Global MG94xREV":0.004108422798314066,
"Nucleotide GTR":0.004027259639267021,
"amino-acid": [
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],
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],
"original name":"epi_isl_433553_Scotland_20200401_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_433621_Scotland_20200404_null_1":{
"Global MG94xREV":0.004102624374890881,
"Nucleotide GTR":0.004021575765486278,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_433621_Scotland_20200404_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_433922_England_20200411_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_433922_England_20200411_null_1",
"synonymous substitution count": [
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]
},
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"Global MG94xREV":0.004102589238415508,
"Nucleotide GTR":0.004021541323142802,
"amino-acid": [
["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "L", "Q", "Q", "L", "R", "V", "E", "S", "S", "S", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "G", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"]
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],
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],
"original name":"epi_isl_433971_England_20200413_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_434030_England_20200414_null_2":{
"Global MG94xREV":0.004104655142085544,
"Nucleotide GTR":0.004023566414248902,
"amino-acid": [
["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "F", "Q", "Q", "L", "R", "V", "E", "S", "S", "S", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "G", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"]
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],
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],
"original name":"epi_isl_434030_England_20200414_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_434172_Washington_20200330_null_16":{
"Global MG94xREV":0.004108520108902431,
"Nucleotide GTR":0.004027355027454712,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_434172_Washington_20200330_null_16",
"synonymous substitution count": [
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]
},
"epi_isl_434383_Antwerp_20200410_null_1":{
"Global MG94xREV":0.004113072834490757,
"Nucleotide GTR":0.004031817812545399,
"amino-acid": [
["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "L", "Q", "Q", "L", "R", "V", "E", "S", "S", "S", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "G", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"]
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"codon": [
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],
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],
"original name":"epi_isl_434383_Antwerp_20200410_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_434971_Texas_20200331_null_6":{
"Global MG94xREV":0.004108500894103416,
"Nucleotide GTR":0.004027336192249982,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_434971_Texas_20200331_null_6",
"synonymous substitution count": [
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]
},
"epi_isl_435019_Texas_20200402_null_11":{
"Global MG94xREV":0.004108422800145477,
"Nucleotide GTR":0.004027259641062261,
"amino-acid": [
["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "L", "Q", "Q", "L", "R", "V", "E", "S", "S", "S", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "G", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"]
],
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_435019_Texas_20200402_null_11",
"synonymous substitution count": [
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]
},
"epi_isl_435389_Utah_20200406_null_28":{
"Global MG94xREV":0.004108481531356665,
"Nucleotide GTR":0.004027317212020261,
"amino-acid": [
["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "L", "Q", "Q", "L", "R", "V", "E", "S", "S", "F", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "G", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"]
],
"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, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_435389_Utah_20200406_null_28",
"synonymous substitution count": [
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]
},
"epi_isl_435412_Baranya_20200330_null_5":{
"Global MG94xREV":0.004108422798398401,
"Nucleotide GTR":0.004027259639349694,
"amino-acid": [
["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "L", "Q", "Q", "L", "R", "V", "E", "S", "S", "S", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "G", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"]
],
"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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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_435412_Baranya_20200330_null_5",
"synonymous substitution count": [
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"Nucleotide GTR":0.004027259638124429,
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"Nucleotide GTR":0.004027355547628555,
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"Nucleotide GTR":0.004028507861784996,
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"Nucleotide GTR":0.004028960545503546,
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"Nucleotide GTR":0,
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"attributes":{
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"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":{
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"display order":1
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"codon":{
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"nonsynonymous substitution count":{
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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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82]
],
"name":"slac.filter.default"
}
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"fits":{
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"Equilibrium frequencies": [
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[0.01487404170559431],
[0.01592735521067367],
[0.02237255052585401],
[0.02202414511199876],
[0.008719376225202219],
[0.009336843683991115],
[0.01311510946475946],
[0.009510554276904519],
[0.003765235854959855],
[0.004031873118343793],
[0.005663418933077451],
[0.03637510575729421],
[0.0144009327361621],
[0.01542074276742172],
[0.02166093128124238],
[0.02659621230784844],
[0.01052946119353091],
[0.011275110822319],
[0.01583771964775977],
[0.01559108047883602],
[0.006172520920156606],
[0.006609631409307682],
[0.009284298033543586],
[0.006732602622054718],
[0.002665442628440367],
[0.002854197425093553],
[0.004009182645771298],
[0.02575024812105758],
[0.01019454331226167],
[0.01091647554570989],
[0.01533395830507846],
[0.04425024194143752],
[0.01751870529282944],
[0.01875930211524539],
[0.02635047871110648],
[0.0259401254333245],
[0.01026971588826252],
[0.01099697150933332],
[0.01544702792583293],
[0.01120156853438725],
[0.004434709718221863],
[0.004748756144187773],
[0.006670397273465902],
[0.04284274377944396],
[0.01696147567286947],
[0.01816261197098734],
[0.02551233074340459],
[0.02054034002857635],
[0.03089542198437613],
[0.03041429077538589],
[0.01204104143632841],
[0.01289373445757594],
[0.01811133875043786],
[0.005199610588665657],
[0.005567823893603163],
[0.007820910611399947],
[0.05023228088363051],
[0.01988699917509118],
[0.02129530804104973],
[0.0299127098510826]
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"Log Likelihood":-807.4625748396833,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.5277639372631927, 1]
]
},
"display order":1,
"estimated parameters":84
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"Nucleotide GTR":{
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"Equilibrium frequencies": [
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[0.1951607611548556],
[0.1845308398950131],
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"Log Likelihood":-823.7754154713507,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.3045658851430875,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.1006787500440949,
"Substitution rate from nucleotide C to nucleotide G":0,
"Substitution rate from nucleotide C to nucleotide T":2.91105246487536,
"Substitution rate from nucleotide G to nucleotide T":0.752011772835393
},
"display order":0,
"estimated parameters":131
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-05/sequences.nsp7.compressed.fas",
"number of sequences":63,
"number of sites":83,
"partition count":1,
"trees":{
"0":"(epi_isl_433971_England_20200413_null_2,epi_isl_431963_Wales_20200330_null_3,epi_isl_434971_Texas_20200331_null_6,epi_isl_430342_New_York_20200330_null_1,epi_isl_430363_New_York_20200408_null_2,epi_isl_435019_Texas_20200402_null_11,(epi_isl_424582_Reykjavik_20200327_null_1,epi_isl_430388_New_York_20200409_null_7)Node58,epi_isl_421487_Portugal_20200322_null_1,epi_isl_435455_Louisiana_20200402_null_1,epi_isl_427377_Liege_20200407_null_2,epi_isl_419839_Victoria_20200316_null_1,epi_isl_430926_Connecticut_20200404_null_1,epi_isl_432224_Wales_20200331_null_1,epi_isl_427473_New_York_20200401_null_1,epi_isl_430225_Washington_20200320_null_2,epi_isl_430429_New_York_20200413_null_2,epi_isl_433289_Scotland_20200323_null_2,epi_isl_435389_Utah_20200406_null_28,epi_isl_421660_Ohio_20200401_null_1,epi_isl_430415_New_York_20200410_null_1,epi_isl_435412_Baranya_20200330_null_5,epi_isl_429644_Washington_20200408_null_4,epi_isl_424597_Reykjavik_20200327_null_2,epi_isl_432537_England_20200320_null_1,epi_isl_433553_Scotland_20200401_null_1,epi_isl_424545_Reykjavik_20200325_null_2,epi_isl_427041_Victoria_20200329_null_1,epi_isl_432861_England_20200401_null_1,epi_isl_424503_Reykjavik_20200320_null_1,(epi_isl_433922_England_20200411_null_1,epi_isl_434383_Antwerp_20200410_null_1)Node112,epi_isl_435457_Louisiana_20200402_null_3,epi_isl_418972_New_York_20200317_null_1,epi_isl_422283_Wales_20200327_null_2,epi_isl_419186_ARA_20200322_null_4,epi_isl_430668_Victoria_20200403_null_2,epi_isl_433621_Scotland_20200404_null_1,epi_isl_421955_England_20200330_null_1,epi_isl_434172_Washington_20200330_null_16,epi_isl_434030_England_20200414_null_2,epi_isl_435578_Louisiana_20200424_null_4,epi_isl_424355_Beijing_20200124_null_1,epi_isl_423486_England_20200331_null_4,epi_isl_428787_New_York_20200406_null_1,epi_isl_422654_Netherlands_20200318_null_1,epi_isl_417445_Lombardy_20200224_null_1,((epi_isl_406799_Wuhan_20191231_null_1,epi_isl_418031_Washington_20200316_null_1)Node16,epi_isl_421751_Luxembourg_20200317_null_3)Node15,epi_isl_426880_Victoria_20200323_null_2,(epi_isl_429678_Minas_gerais_20200316_null_7,epi_isl_430362_New_York_20200408_null_2)Node28,(epi_isl_420300_New_York_20200318_null_1,epi_isl_433206_Scotland_20200402_null_2)Node24,epi_isl_435547_New_York_20200424_null_213,epi_isl_422544_New_York_20200320_null_1,epi_isl_435642_California_20200312_null_1,epi_isl_435671_California_20200321_null_15701,epi_isl_429534_Unknown_20200325_null_1,epi_isl_426102_Washington_20200325_null_3,epi_isl_432546_England_20200321_null_3,epi_isl_432731_England_20200402_null_3)"
}
},
"tested":{
"0":{
"Node112":"test",
"Node15":"test",
"Node16":"test",
"Node24":"test",
"Node28":"test",
"Node58":"test",
"epi_isl_406799_Wuhan_20191231_null_1":"test",
"epi_isl_417445_Lombardy_20200224_null_1":"test",
"epi_isl_418031_Washington_20200316_null_1":"test",
"epi_isl_418972_New_York_20200317_null_1":"test",
"epi_isl_419186_ARA_20200322_null_4":"test",
"epi_isl_419839_Victoria_20200316_null_1":"test",
"epi_isl_420300_New_York_20200318_null_1":"test",
"epi_isl_421487_Portugal_20200322_null_1":"test",
"epi_isl_421660_Ohio_20200401_null_1":"test",
"epi_isl_421751_Luxembourg_20200317_null_3":"test",
"epi_isl_421955_England_20200330_null_1":"test",
"epi_isl_422283_Wales_20200327_null_2":"test",
"epi_isl_422544_New_York_20200320_null_1":"test",
"epi_isl_422654_Netherlands_20200318_null_1":"test",
"epi_isl_423486_England_20200331_null_4":"test",
"epi_isl_424355_Beijing_20200124_null_1":"test",
"epi_isl_424503_Reykjavik_20200320_null_1":"test",
"epi_isl_424545_Reykjavik_20200325_null_2":"test",
"epi_isl_424582_Reykjavik_20200327_null_1":"test",
"epi_isl_424597_Reykjavik_20200327_null_2":"test",
"epi_isl_426102_Washington_20200325_null_3":"test",
"epi_isl_426880_Victoria_20200323_null_2":"test",
"epi_isl_427041_Victoria_20200329_null_1":"test",
"epi_isl_427377_Liege_20200407_null_2":"test",
"epi_isl_427473_New_York_20200401_null_1":"test",
"epi_isl_428787_New_York_20200406_null_1":"test",
"epi_isl_429534_Unknown_20200325_null_1":"test",
"epi_isl_429644_Washington_20200408_null_4":"test",
"epi_isl_429678_Minas_gerais_20200316_null_7":"test",
"epi_isl_430225_Washington_20200320_null_2":"test",
"epi_isl_430342_New_York_20200330_null_1":"test",
"epi_isl_430362_New_York_20200408_null_2":"test",
"epi_isl_430363_New_York_20200408_null_2":"test",
"epi_isl_430388_New_York_20200409_null_7":"test",
"epi_isl_430415_New_York_20200410_null_1":"test",
"epi_isl_430429_New_York_20200413_null_2":"test",
"epi_isl_430668_Victoria_20200403_null_2":"test",
"epi_isl_430926_Connecticut_20200404_null_1":"test",
"epi_isl_431963_Wales_20200330_null_3":"test",
"epi_isl_432224_Wales_20200331_null_1":"test",
"epi_isl_432537_England_20200320_null_1":"test",
"epi_isl_432546_England_20200321_null_3":"test",
"epi_isl_432731_England_20200402_null_3":"test",
"epi_isl_432861_England_20200401_null_1":"test",
"epi_isl_433206_Scotland_20200402_null_2":"test",
"epi_isl_433289_Scotland_20200323_null_2":"test",
"epi_isl_433553_Scotland_20200401_null_1":"test",
"epi_isl_433621_Scotland_20200404_null_1":"test",
"epi_isl_433922_England_20200411_null_1":"test",
"epi_isl_433971_England_20200413_null_2":"test",
"epi_isl_434030_England_20200414_null_2":"test",
"epi_isl_434172_Washington_20200330_null_16":"test",
"epi_isl_434383_Antwerp_20200410_null_1":"test",
"epi_isl_434971_Texas_20200331_null_6":"test",
"epi_isl_435019_Texas_20200402_null_11":"test",
"epi_isl_435389_Utah_20200406_null_28":"test",
"epi_isl_435412_Baranya_20200330_null_5":"test",
"epi_isl_435455_Louisiana_20200402_null_1":"test",
"epi_isl_435457_Louisiana_20200402_null_3":"test",
"epi_isl_435547_New_York_20200424_null_213":"test",
"epi_isl_435578_Louisiana_20200424_null_4":"test",
"epi_isl_435642_California_20200312_null_1":"test",
"epi_isl_435671_California_20200321_null_15701":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":0
},
"Total time":{
"order":0,
"timer":2
}
}
}