{
"MLE":{
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"NAMES": [
["epi_isl_416620_unknown_20200217_null_1"],
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]
}
}
},
"headers": [
["ES", "Expected synonymous sites"],
["EN", "Expected non-synonymous sites"],
["S", "Inferred synonymous substitutions"],
["N", "Inferred non-synonymous substitutions"],
["P[S]", "Expected proportion of synonymous sites"],
["dS", "Inferred synonymous susbsitution rate"],
["dN", "Inferred non-synonymous susbsitution rate"],
["dN-dS", "Scaled by the length of the tested branches"],
["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"],
["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
]
},
"analysis":{
"authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
"citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
"contact":"spond@temple.edu",
"info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.00"
},
"branch attributes":{
"0":{
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"Global MG94xREV":0.005519815643395696,
"Nucleotide GTR":0.005475654573623474,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "I", "I"]
],
"codon": [
["ATG", "TTT", "CAT", "CTC", "GTT", "GAC", "TTT", "CAG", "GTT", "ACT", "ATA", "GCA", "GAG", "ATA", "TTA", "CTA", "ATT", "ATT", "ATG", "AGG", "ACT", "TTT", "AAA", "GTT", "TCC", "ATT", "TGG", "AAT", "CTT", "GAT", "TAC", "ATC", "ATA", "AAC", "CTC", "ATA", "ATT", "AAA", "AAT", "TTA", "TCT", "AAG", "TCA", "CTA", "ACT", "GAG", "AAT", "AAA", "TAT", "TCT", "CAA", "TTA", "GAT", "GAA", "GAG", "CAA", "CCA", "ATG", "GAG", "ATT", "GAC", "ATT", "ATT"]
],
"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]
],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0]
]
},
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"Nucleotide GTR":0.005475518835405117,
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],
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],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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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"Nucleotide GTR":0.005473204536360776,
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],
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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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]
],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"Node32":{
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["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "I", "I"]
],
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},
"epi_isl_414010_England_20200226_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "LF", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
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],
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],
"original name":"epi_isl_414010_England_20200226_null_1",
"synonymous substitution count": [
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]
},
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"Global MG94xREV":0.005541577007397407,
"Nucleotide GTR":0.005497241836681216,
"amino-acid": [
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],
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_415655_Wales_20200312_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416620_unknown_20200217_null_1":{
"Global MG94xREV":0.005541577004354395,
"Nucleotide GTR":0.005497241833662561,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416620_unknown_20200217_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416636_Washington_20200312_null_1":{
"Global MG94xREV":0.005558718918491586,
"Nucleotide GTR":0.005514246604584259,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416636_Washington_20200312_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_417354_Washington_20200313_null_4847":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417354_Washington_20200313_null_4847",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005519281660238927,
"Nucleotide GTR":0.005475124862578126,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417356_Washington_20200313_null_2",
"synonymous substitution count": [
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]
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"epi_isl_417363_Washington_20200314_null_23":{
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"Nucleotide GTR":0,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417363_Washington_20200314_null_23",
"synonymous substitution count": [
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]
},
"epi_isl_417368_USA_20200313_null_1":{
"Global MG94xREV":0.00554155570571769,
"Nucleotide GTR":0.005497220705424762,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
[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]
],
"original name":"epi_isl_417368_USA_20200313_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_417378_Washington_20200314_null_8":{
"Global MG94xREV":0.005541555752070635,
"Nucleotide GTR":0.005497220751406866,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417378_Washington_20200314_null_8",
"synonymous substitution count": [
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]
},
"epi_isl_417952_Madrid_20200309_null_1":{
"Global MG94xREV":0.03528898335131313,
"Nucleotide GTR":0.03500665521634494,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_417952_Madrid_20200309_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418099_Wales_20200313_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_418099_Wales_20200313_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_418141_Wales_20200313_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "TPAS", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_418141_Wales_20200313_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_418210_Touba_20200310_null_6":{
"Global MG94xREV":0.005541566406236125,
"Nucleotide GTR":0.005497231320334117,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "S", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"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, 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_418210_Touba_20200310_null_6",
"synonymous substitution count": [
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]
},
"epi_isl_418305_South_Yorkshire_20200325_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418305_South_Yorkshire_20200325_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418311_Derbyshire_20200325_null_1":{
"Global MG94xREV":0.005536815664333085,
"Nucleotide GTR":0.005492518586556383,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418311_Derbyshire_20200325_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418431_ARA_20200318_null_1":{
"Global MG94xREV":0.005541566374990959,
"Nucleotide GTR":0.005497231289338928,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418431_ARA_20200318_null_1",
"synonymous substitution count": [
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]
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"epi_isl_418750_England_20200318_null_1":{
"Global MG94xREV":0.005536826189214613,
"Nucleotide GTR":0.00549252902723401,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418750_England_20200318_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_418861_Barcelona_20200324_null_1":{
"Global MG94xREV":0.005509860479964796,
"Nucleotide GTR":0.005465779056089332,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418861_Barcelona_20200324_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_419184_ARA_20200322_null_1":{
"Global MG94xREV":0.005517436475639879,
"Nucleotide GTR":0.00547329444030649,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "T", "I", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_419184_ARA_20200322_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_419546_Duesseldorf_20200315_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "KTRI", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"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, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_419546_Duesseldorf_20200315_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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_419595_Luxembourg_20200312_null_2":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "F", "H", "L", "V", "D", "F", "Q", "V", "T", "I", "A", "E", "I", "L", "L", "I", "I", "M", "R", "T", "F", "K", "V", "S", "I", "W", "N", "L", "D", "Y", "I", "T", "N", "L", "I", "I", "K", "N", "L", "S", "K", "S", "L", "T", "E", "N", "K", "Y", "S", "Q", "L", "D", "E", "E", "Q", "P", "M", "E", "I", "D", "-", "-"]
],
"codon": [
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],
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],
"original name":"epi_isl_419595_Luxembourg_20200312_null_2",
"synonymous substitution count": [
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]
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"epi_isl_419875_Victoria_20200318_null_1":{
"Global MG94xREV":0.005517472214956757,
"Nucleotide GTR":0.005473329893692367,
"amino-acid": [
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],
"original name":"epi_isl_419875_Victoria_20200318_null_1",
"synonymous substitution count": [
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]
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"Global MG94xREV":0.005541566338801272,
"Nucleotide GTR":0.005497231253438768,
"amino-acid": [
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],
"original name":"epi_isl_419898_Victoria_20200319_null_1",
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]
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"epi_isl_420063_Ile_de_France_20200322_null_2":{
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"Nucleotide GTR":0.005492529084054417,
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],
"original name":"epi_isl_420063_Ile_de_France_20200322_null_2",
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"epi_isl_420168_South_Yorkshire_20200325_null_1":{
"Global MG94xREV":0.005517460325608323,
"Nucleotide GTR":0.0054733180994642,
"amino-acid": [
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],
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],
"original name":"epi_isl_420168_South_Yorkshire_20200325_null_1",
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]
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"epi_isl_420198_South_Yorkshire_20200328_null_1":{
"Global MG94xREV":0.01120599542472661,
"Nucleotide GTR":0.01111634229538513,
"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, 2, 0, 0]
],
"original name":"epi_isl_420198_South_Yorkshire_20200328_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_420388_Vilvoorde_20200324_null_2":{
"Global MG94xREV":0.005536835456318265,
"Nucleotide GTR":0.005492538220196562,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_420388_Vilvoorde_20200324_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_420485_England_20200318_null_2":{
"Global MG94xREV":0.005541566379789749,
"Nucleotide GTR":0.005497231294099318,
"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, 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]
],
"original name":"epi_isl_420485_England_20200318_null_2",
"synonymous substitution count": [
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]
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"epi_isl_421323_Wisconsin_20200322_null_2":{
"Global MG94xREV":0.005509999054497615,
"Nucleotide GTR":0.00546591652196201,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_421323_Wisconsin_20200322_null_2",
"synonymous substitution count": [
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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":{
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"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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]
],
"name":"slac.filter.default"
}
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"fits":{
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"Equilibrium frequencies": [
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[0.01855068011006908],
[0.03168929999318071],
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[0.01810446470785697],
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[0.04451890617027147]
],
"Log Likelihood":-421.3091630636041,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[1.358626950734209, 1]
]
},
"display order":1,
"estimated parameters":47
},
"Nucleotide GTR":{
"AIC-c":994.1445956742874,
"Equilibrium frequencies": [
[0.3606403013182674],
[0.1429378531073446],
[0.14030131826742],
[0.3561205273069679]
],
"Log Likelihood":-433.327974410893,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.2335358396681815,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.1934691232428405,
"Substitution rate from nucleotide C to nucleotide G":1.220549059675838,
"Substitution rate from nucleotide C to nucleotide T":2.980014404418363,
"Substitution rate from nucleotide G to nucleotide T":2.271483991614351
},
"display order":0,
"estimated parameters":63
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-09/sequences.ORF6.compressed.fas",
"number of sequences":29,
"number of sites":63,
"partition count":1,
"trees":{
"0":"(epi_isl_416620_unknown_20200217_null_1,epi_isl_418861_Barcelona_20200324_null_1,epi_isl_419898_Victoria_20200319_null_1,epi_isl_421323_Wisconsin_20200322_null_2,epi_isl_418431_ARA_20200318_null_1,epi_isl_418750_England_20200318_null_1,epi_isl_418210_Touba_20200310_null_6,epi_isl_418311_Derbyshire_20200325_null_1,epi_isl_420063_Ile_de_France_20200322_null_2,epi_isl_420485_England_20200318_null_2,epi_isl_416636_Washington_20200312_null_1,epi_isl_419875_Victoria_20200318_null_1,epi_isl_420168_South_Yorkshire_20200325_null_1,epi_isl_417378_Washington_20200314_null_8,epi_isl_420388_Vilvoorde_20200324_null_2,epi_isl_417368_USA_20200313_null_1,epi_isl_415655_Wales_20200312_null_1,epi_isl_419184_ARA_20200322_null_1,(epi_isl_419546_Duesseldorf_20200315_null_1,epi_isl_419595_Luxembourg_20200312_null_2)Node26,(epi_isl_414010_England_20200226_null_1,epi_isl_418305_South_Yorkshire_20200325_null_1)Node23,epi_isl_418099_Wales_20200313_null_1,epi_isl_418141_Wales_20200313_null_1,(epi_isl_417356_Washington_20200313_null_2,epi_isl_417363_Washington_20200314_null_23,epi_isl_417952_Madrid_20200309_null_1,epi_isl_420198_South_Yorkshire_20200328_null_1)Node13,epi_isl_417354_Washington_20200313_null_4847)"
}
},
"tested":{
"0":{
"Node13":"test",
"Node23":"test",
"Node26":"test",
"epi_isl_414010_England_20200226_null_1":"test",
"epi_isl_415655_Wales_20200312_null_1":"test",
"epi_isl_416620_unknown_20200217_null_1":"test",
"epi_isl_416636_Washington_20200312_null_1":"test",
"epi_isl_417354_Washington_20200313_null_4847":"test",
"epi_isl_417356_Washington_20200313_null_2":"test",
"epi_isl_417363_Washington_20200314_null_23":"test",
"epi_isl_417368_USA_20200313_null_1":"test",
"epi_isl_417378_Washington_20200314_null_8":"test",
"epi_isl_417952_Madrid_20200309_null_1":"test",
"epi_isl_418099_Wales_20200313_null_1":"test",
"epi_isl_418141_Wales_20200313_null_1":"test",
"epi_isl_418210_Touba_20200310_null_6":"test",
"epi_isl_418305_South_Yorkshire_20200325_null_1":"test",
"epi_isl_418311_Derbyshire_20200325_null_1":"test",
"epi_isl_418431_ARA_20200318_null_1":"test",
"epi_isl_418750_England_20200318_null_1":"test",
"epi_isl_418861_Barcelona_20200324_null_1":"test",
"epi_isl_419184_ARA_20200322_null_1":"test",
"epi_isl_419546_Duesseldorf_20200315_null_1":"test",
"epi_isl_419595_Luxembourg_20200312_null_2":"test",
"epi_isl_419875_Victoria_20200318_null_1":"test",
"epi_isl_419898_Victoria_20200319_null_1":"test",
"epi_isl_420063_Ile_de_France_20200322_null_2":"test",
"epi_isl_420168_South_Yorkshire_20200325_null_1":"test",
"epi_isl_420198_South_Yorkshire_20200328_null_1":"test",
"epi_isl_420388_Vilvoorde_20200324_null_2":"test",
"epi_isl_420485_England_20200318_null_2":"test",
"epi_isl_421323_Wisconsin_20200322_null_2":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}