{
"MLE":{
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"NAMES": [
["epi_isl_413602_Helsinki_20200303_null_1"],
["epi_isl_416373_Shanghai_20200207_null_1"],
["epi_isl_417011_Li_ge_20200307_null_3"],
["epi_isl_416414_Victoria_20200306_null_1"],
["epi_isl_417202_Wisconsin_20200321_null_1"],
["epi_isl_419263_Virginia_20200310_null_2582"],
["epi_isl_416489_Wisconsin_20200315_null_1"],
["epi_isl_416677_Washington_20200312_null_1"],
["epi_isl_413860_Guangdong_20200130_null_1"],
["epi_isl_418113_Wales_20200313_null_1"],
["Node45"],
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["epi_isl_414480_USA_20200221_null_1"],
["epi_isl_418306_South_Yorkshire_20200325_null_1"],
["epi_isl_413926_California_20200305_null_1"],
["epi_isl_414934_Shandong_20200121_null_1"],
["epi_isl_417385_New_South_Wales_20200306_null_2"],
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["epi_isl_416625_unknown_20200217_null_3"],
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["epi_isl_414937_Shandong_20200126_null_1"],
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["Node13"]
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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":0.009300649956295747,
"Nucleotide GTR":0.008831237500688793,
"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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],
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],
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"Nucleotide GTR":0.02148548848935267,
"amino-acid": [
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],
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],
"nonsynonymous substitution count": [
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],
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[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]
]
},
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"Nucleotide GTR":0.004293889607989204,
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["R", "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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],
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],
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]
},
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"Nucleotide GTR":0.008967763008773791,
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],
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],
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],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
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],
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],
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],
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]
},
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"Global MG94xREV":2.212409787745347,
"Nucleotide GTR":2.100747407572505,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "Y", "N", "Y", "-", "-", "-", "-", "-", "-", "L", "N", "S", "G", "L", "N", "S", "C", "R", "P", "H"]
],
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],
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],
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]
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],
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"Nucleotide GTR":0.005951757742773217,
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]
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"Global MG94xREV":0.009297137400243915,
"Nucleotide GTR":0.008827902226608595,
"amino-acid": [
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],
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]
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"epi_isl_413860_Guangdong_20200130_null_1":{
"Global MG94xREV":0.003015027582655894,
"Nucleotide GTR":0.002862856335705649,
"amino-acid": [
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],
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]
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"epi_isl_413926_California_20200305_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_413926_California_20200305_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414480_USA_20200221_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_414480_USA_20200221_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414934_Shandong_20200121_null_1":{
"Global MG94xREV":0.009284209744361725,
"Nucleotide GTR":0.008815627041545263,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_414934_Shandong_20200121_null_1",
"synonymous substitution count": [
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]
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"epi_isl_414937_Shandong_20200126_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_414937_Shandong_20200126_null_1",
"synonymous substitution count": [
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]
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"epi_isl_415435_Wales_20200306_null_1":{
"Global MG94xREV":1.93111720186091,
"Nucleotide GTR":1.833651920181671,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_415435_Wales_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416373_Shanghai_20200207_null_1":{
"Global MG94xREV":0.009297635350354961,
"Nucleotide GTR":0.008828375044714292,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_416373_Shanghai_20200207_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416414_Victoria_20200306_null_1":{
"Global MG94xREV":0.009298133299494781,
"Nucleotide GTR":0.008828847861897788,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416414_Victoria_20200306_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416489_Wisconsin_20200315_null_1":{
"Global MG94xREV":0.009301642186899793,
"Nucleotide GTR":0.008832179652491175,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_416489_Wisconsin_20200315_null_1",
"synonymous substitution count": [
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]
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"epi_isl_416567_unknown_20200215_null_1":{
"Global MG94xREV":0.02221216151447522,
"Nucleotide GTR":0.02109109305906147,
"amino-acid": [
["R", "W", "A", "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_416567_unknown_20200215_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_416604_unknown_20200216_null_1":{
"Global MG94xREV":0.02288241295545243,
"Nucleotide GTR":0.02172751628628357,
"amino-acid": [
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"codon": [
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"nonsynonymous substitution count": [
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"original name":"epi_isl_416604_unknown_20200216_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_416624_unknown_20200217_null_13":{
"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_416624_unknown_20200217_null_13",
"synonymous substitution count": [
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]
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"epi_isl_416625_unknown_20200217_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_416625_unknown_20200217_null_3",
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]
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"Global MG94xREV":0.009301553212029089,
"Nucleotide GTR":0.008832095168264983,
"amino-acid": [
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],
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"original name":"epi_isl_416677_Washington_20200312_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417011_Li_ge_20200307_null_3":{
"Global MG94xREV":0.009238614285434437,
"Nucleotide GTR":0.008772332827847087,
"amino-acid": [
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"original name":"epi_isl_417011_Li_ge_20200307_null_3",
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]
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"epi_isl_417202_Wisconsin_20200321_null_1":{
"Global MG94xREV":0.009295732397627177,
"Nucleotide GTR":0.008826568135780989,
"amino-acid": [
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"original name":"epi_isl_417202_Wisconsin_20200321_null_1",
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]
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"epi_isl_417222_England_20200304_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_417222_England_20200304_null_1",
"synonymous substitution count": [
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]
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"epi_isl_417385_New_South_Wales_20200306_null_2":{
"Global MG94xREV":0.009295507966590578,
"Nucleotide GTR":0.008826355031987589,
"amino-acid": [
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],
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"original name":"epi_isl_417385_New_South_Wales_20200306_null_2",
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"epi_isl_418082_Washington_20200315_null_2":{
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"Nucleotide GTR":1.10957712656878,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_418082_Washington_20200315_null_2",
"synonymous substitution count": [
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]
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"epi_isl_418113_Wales_20200313_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_418113_Wales_20200313_null_1",
"synonymous substitution count": [
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"epi_isl_418182_Madrid_20200312_null_3":{
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"Nucleotide GTR":0.03209250923695003,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_418182_Madrid_20200312_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_418306_South_Yorkshire_20200325_null_1":{
"Global MG94xREV":0.009295332094683114,
"Nucleotide GTR":0.008826188036498896,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418306_South_Yorkshire_20200325_null_1",
"synonymous substitution count": [
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"epi_isl_418999_Singapore_20200301_null_4":{
"Global MG94xREV":1853.725359186684,
"Nucleotide GTR":1760.166115804161,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_418999_Singapore_20200301_null_4",
"synonymous substitution count": [
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]
},
"epi_isl_419263_Virginia_20200310_null_2582":{
"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", "-", "-", "-", "-", "-"]
],
"codon": [
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],
"nonsynonymous substitution count": [
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"original name":"epi_isl_419263_Virginia_20200310_null_2582",
"synonymous substitution count": [
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]
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"epi_isl_419297_Chiba_20200310_null_61":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "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_419297_Chiba_20200310_null_61",
"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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"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
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"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":814.4744651747998,
"Equilibrium frequencies": [
[0.03138130651682453],
[0.02254959999901194],
[0.01426033495230907],
[0.03684887244474039],
[0.01624169231003801],
[0.0116707589820083],
[0.00738057137325719],
[0.0190714828236499],
[0.01540915995655368],
[0.01107252794445596],
[0.007002250916364939],
[0.01809389833451409],
[0.0461896228394075],
[0.0331903809860642],
[0.0209895497071684],
[0.05423724214182983],
[0.01384417412112325],
[0.009947979335424796],
[0.006291087976195696],
[0.0162562449724183],
[0.007165183394812571],
[0.005148670893799849],
[0.003256012146912028],
[0.008413573501698088],
[0.006797903502978674],
[0.004884755347641994],
[0.003089112331061747],
[0.007982302423852766],
[0.02037700950516304],
[0.01464226523746364],
[0.00925974770088746],
[0.02392729645142244],
[0.01784419512448514],
[0.01282226608843486],
[0.008108782828818552],
[0.02095318974908466],
[0.009235432137817023],
[0.00663628521693771],
[0.004196777328056171],
[0.01084452174214039],
[0.008762033436107246],
[0.006296116098807339],
[0.003981654861795872],
[0.0102886427711531],
[0.02626457385484807],
[0.0188728800776285],
[0.01193518250583318],
[0.030840651305384],
[0.01964005393737786],
[0.03209430953888179],
[0.01414604751381039],
[0.0101648958698524],
[0.006428265683905242],
[0.01661071377490828],
[0.009643853818327925],
[0.00609875943194056],
[0.01575926576271239],
[0.04022983485085557],
[0.02890786855629297],
[0.01828129494040354],
[0.04723908012234522]
],
"Log Likelihood":-357.0892873819204,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.7480729841336983, 1]
]
},
"display order":1,
"estimated parameters":48
},
"Nucleotide GTR":{
"AIC-c":837.2497532468586,
"Equilibrium frequencies": [
[0.3007563694267516],
[0.1813296178343949],
[0.1578423566878981],
[0.3600716560509554]
],
"Log Likelihood":-360.6450307431685,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.2124689112305793,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.07189245452826301,
"Substitution rate from nucleotide C to nucleotide G":0.5415552485709323,
"Substitution rate from nucleotide C to nucleotide T":1.716374546936278,
"Substitution rate from nucleotide G to nucleotide T":0.4512025720723484
},
"display order":0,
"estimated parameters":57
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-02/sequences.ORF10.compressed.fas",
"number of sequences":26,
"number of sites":44,
"partition count":1,
"trees":{
"0":"(epi_isl_413602_Helsinki_20200303_null_1,epi_isl_416373_Shanghai_20200207_null_1,epi_isl_417011_Li_ge_20200307_null_3,epi_isl_416414_Victoria_20200306_null_1,epi_isl_417202_Wisconsin_20200321_null_1,epi_isl_419263_Virginia_20200310_null_2582,epi_isl_416489_Wisconsin_20200315_null_1,epi_isl_416677_Washington_20200312_null_1,(epi_isl_413860_Guangdong_20200130_null_1,epi_isl_418113_Wales_20200313_null_1)Node45,epi_isl_417222_England_20200304_null_1,epi_isl_414480_USA_20200221_null_1,epi_isl_418306_South_Yorkshire_20200325_null_1,epi_isl_413926_California_20200305_null_1,epi_isl_414934_Shandong_20200121_null_1,epi_isl_417385_New_South_Wales_20200306_null_2,(epi_isl_416624_unknown_20200217_null_13,epi_isl_416625_unknown_20200217_null_3)Node10,(((epi_isl_418182_Madrid_20200312_null_3,epi_isl_416567_unknown_20200215_null_1,epi_isl_419297_Chiba_20200310_null_61)Node15,epi_isl_416604_unknown_20200216_null_1)Node14,((epi_isl_418082_Washington_20200315_null_2,epi_isl_418999_Singapore_20200301_null_4)Node23,epi_isl_414937_Shandong_20200126_null_1)Node22,epi_isl_415435_Wales_20200306_null_1)Node13)"
}
},
"tested":{
"0":{
"Node10":"test",
"Node13":"test",
"Node14":"test",
"Node15":"test",
"Node22":"test",
"Node23":"test",
"Node45":"test",
"epi_isl_413602_Helsinki_20200303_null_1":"test",
"epi_isl_413860_Guangdong_20200130_null_1":"test",
"epi_isl_413926_California_20200305_null_1":"test",
"epi_isl_414480_USA_20200221_null_1":"test",
"epi_isl_414934_Shandong_20200121_null_1":"test",
"epi_isl_414937_Shandong_20200126_null_1":"test",
"epi_isl_415435_Wales_20200306_null_1":"test",
"epi_isl_416373_Shanghai_20200207_null_1":"test",
"epi_isl_416414_Victoria_20200306_null_1":"test",
"epi_isl_416489_Wisconsin_20200315_null_1":"test",
"epi_isl_416567_unknown_20200215_null_1":"test",
"epi_isl_416604_unknown_20200216_null_1":"test",
"epi_isl_416624_unknown_20200217_null_13":"test",
"epi_isl_416625_unknown_20200217_null_3":"test",
"epi_isl_416677_Washington_20200312_null_1":"test",
"epi_isl_417011_Li_ge_20200307_null_3":"test",
"epi_isl_417202_Wisconsin_20200321_null_1":"test",
"epi_isl_417222_England_20200304_null_1":"test",
"epi_isl_417385_New_South_Wales_20200306_null_2":"test",
"epi_isl_418082_Washington_20200315_null_2":"test",
"epi_isl_418113_Wales_20200313_null_1":"test",
"epi_isl_418182_Madrid_20200312_null_3":"test",
"epi_isl_418306_South_Yorkshire_20200325_null_1":"test",
"epi_isl_418999_Singapore_20200301_null_4":"test",
"epi_isl_419263_Virginia_20200310_null_2582":"test",
"epi_isl_419297_Chiba_20200310_null_61":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":1
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":3
}
}
}