{
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},
"headers": [
["alpha;", "Synonymous substitution rate at a site"],
["β-", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
["p-", "Mixture distribution weight allocated to β-; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
["β+", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
["p+", "Mixture distribution weight allocated to β+; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"],
["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"],
["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
["MEME LogL", "Site Log-likelihood under the MEME model"],
["FEL LogL", "Site Log-likelihood under the FEL model"]
]
},
"analysis":{
"authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
"citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
"contact":"spond@temple.edu",
"info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. 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":"2.1.2"
},
"branch attributes":{
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"Nucleotide GTR":0,
"original name":"epi_isl_423033_Washington_20200318_null_6099"
}
},
"attributes":{
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"EBF site 106 (partition 1)":{
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"EBF site 107 (partition 1)":{
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"EBF site 112 (partition 1)":{
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"EBF site 13 (partition 1)":{
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"EBF site 16 (partition 1)":{
"attribute type":"branch label",
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"EBF site 19 (partition 1)":{
"attribute type":"branch label",
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},
"EBF site 20 (partition 1)":{
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"EBF site 21 (partition 1)":{
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"EBF site 23 (partition 1)":{
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"EBF site 24 (partition 1)":{
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"EBF site 25 (partition 1)":{
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"EBF site 28 (partition 1)":{
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"EBF site 30 (partition 1)":{
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"EBF site 31 (partition 1)":{
"attribute type":"branch label",
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"EBF site 32 (partition 1)":{
"attribute type":"branch label",
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"EBF site 34 (partition 1)":{
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"EBF site 36 (partition 1)":{
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"EBF site 37 (partition 1)":{
"attribute type":"branch label",
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},
"EBF site 42 (partition 1)":{
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},
"EBF site 44 (partition 1)":{
"attribute type":"branch label",
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},
"EBF site 45 (partition 1)":{
"attribute type":"branch label",
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},
"EBF site 49 (partition 1)":{
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"EBF site 61 (partition 1)":{
"attribute type":"branch label",
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"EBF site 64 (partition 1)":{
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"EBF site 65 (partition 1)":{
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"EBF site 67 (partition 1)":{
"attribute type":"branch label",
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"EBF site 68 (partition 1)":{
"attribute type":"branch label",
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"EBF site 71 (partition 1)":{
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"EBF site 77 (partition 1)":{
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},
"EBF site 80 (partition 1)":{
"attribute type":"branch label",
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"EBF site 93 (partition 1)":{
"attribute type":"branch label",
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},
"EBF site 95 (partition 1)":{
"attribute type":"branch label",
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"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
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},
"original name":{
"attribute type":"node label",
"display order":-1
}
}
},
"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, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112]
],
"name":"meme.filter.default"
}
},
"fits":{
"Global MG94xREV":{
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"Equilibrium frequencies": [
[0.0340074262827242],
[0.01158710866119235],
[0.01443203611397728],
[0.03931298108078487],
[0.02814247174489953],
[0.009588784384672477],
[0.01194307282128261],
[0.03253302528912021],
[0.02255668097152955],
[0.007685577593554532],
[0.009572580755926024],
[0.02607578606233784],
[0.0274544690837353],
[0.009354366127676969],
[0.01165109896916317],
[0.03173768619532883],
[0.01830490731707057],
[0.006236900974293927],
[0.007768217484813648],
[0.02116068617068747],
[0.01514802480731561],
[0.005161278833204982],
[0.006428502976294331],
[0.01751129320138466],
[0.01214140556041814],
[0.004136854825724857],
[0.005152557034620809],
[0.01403560631500452],
[0.01477769907781732],
[0.005035100379356158],
[0.006271344529265092],
[0.01708319234257636],
[0.03120216723139835],
[0.0106312926820508],
[0.01324154320218751],
[0.03607006892699164],
[0.02582101045780512],
[0.008797809379310807],
[0.01095789350033039],
[0.02984938898860784],
[0.02069598934090775],
[0.007051597358480451],
[0.008782942381446897],
[0.02392480485418421],
[0.02518976086217786],
[0.008582728190982759],
[0.0106900044549999],
[0.02911965709993639],
[0.00882231960024436],
[0.02993254777135697],
[0.02142742312462282],
[0.007300813593190895],
[0.009093347488078603],
[0.02477035083175926],
[0.005851729178125938],
[0.007288476297005551],
[0.01985386736209904],
[0.02090358412905541],
[0.007122329655237235],
[0.008871041241228662],
[0.02416478684844245]
],
"Log Likelihood":-711.7425023912681,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *background*": [
[0.380131045747916, 1]
]
},
"display order":1,
"estimated parameters":51
},
"Nucleotide GTR":{
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"Equilibrium frequencies": [
[0.309406751884628],
[0.1879711569977057],
[0.2123893805309734],
[0.2902327105866929]
],
"Log Likelihood":-732.4248171277411,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.8009754353875468,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.2033600333667581,
"Substitution rate from nucleotide C to nucleotide G":0.2316914787608659,
"Substitution rate from nucleotide C to nucleotide T":3.41711093006563,
"Substitution rate from nucleotide G to nucleotide T":0.3016920301632587
},
"display order":0,
"estimated parameters":77
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-12/sequences.nsp9.compressed.fas",
"number of sequences":36,
"number of sites":113,
"partition count":1,
"trees":{
"0":"(epi_isl_422905_Zuid_Holland_20200313_null_3,epi_isl_418926_Washington_20200314_null_2,epi_isl_420901_Munich_20200312_null_5,epi_isl_413221_Scotland_20200302_null_1,epi_isl_420239_South_Yorkshire_20200323_null_1,epi_isl_422635_Zuid_Holland_20200331_null_1,epi_isl_421251_Jiangxi_20200203_null_5,epi_isl_416566_unknown_20200215_null_1,epi_isl_415654_Hauts_de_France_20200309_null_1,epi_isl_420664_England_20200326_null_1,epi_isl_418396_Finland_20200313_null_1,epi_isl_421651_Taipei_20200322_null_1,epi_isl_420352_Sint_Gillis_Waas_20200307_null_2,epi_isl_422302_Wales_20200327_null_1,epi_isl_422964_Washington_20200316_null_1,epi_isl_419885_Victoria_20200319_null_1,epi_isl_415621_Washington_20200309_null_1,epi_isl_420589_New_York_20200318_null_1,epi_isl_422125_Wales_20200328_null_1,epi_isl_419953_Victoria_20200321_null_2,epi_isl_421654_Latvia_20200325_null_3,epi_isl_422954_Zuid_Holland_20200327_null_27,epi_isl_422774_Netherlands_20200327_null_5,epi_isl_422289_Wales_20200325_null_5,epi_isl_417176_Hong_Kong_20200121_null_1,epi_isl_416502_Bretagne_20200226_null_1,epi_isl_423033_Washington_20200318_null_6099,epi_isl_416355_Shanghai_20200204_null_2,epi_isl_421572_KZN_20200323_null_1,epi_isl_421510_Hauts_de_France_20200323_null_3,epi_isl_419663_Austria_20200315_null_2,epi_isl_413890_Guangdong_20200228_null_1,epi_isl_415710_Saint_Petersburg_20200315_null_1,epi_isl_419253_Hong_Kong_20200226_null_1,epi_isl_422349_Wales_20200324_null_2,epi_isl_422977_Washington_20200317_null_3)"
}
},
"tested":{
"0":{
"epi_isl_413221_Scotland_20200302_null_1":"background",
"epi_isl_413890_Guangdong_20200228_null_1":"background",
"epi_isl_415621_Washington_20200309_null_1":"background",
"epi_isl_415654_Hauts_de_France_20200309_null_1":"background",
"epi_isl_415710_Saint_Petersburg_20200315_null_1":"background",
"epi_isl_416355_Shanghai_20200204_null_2":"background",
"epi_isl_416502_Bretagne_20200226_null_1":"background",
"epi_isl_416566_unknown_20200215_null_1":"background",
"epi_isl_417176_Hong_Kong_20200121_null_1":"background",
"epi_isl_418396_Finland_20200313_null_1":"background",
"epi_isl_418926_Washington_20200314_null_2":"background",
"epi_isl_419253_Hong_Kong_20200226_null_1":"background",
"epi_isl_419663_Austria_20200315_null_2":"background",
"epi_isl_419885_Victoria_20200319_null_1":"background",
"epi_isl_419953_Victoria_20200321_null_2":"background",
"epi_isl_420239_South_Yorkshire_20200323_null_1":"background",
"epi_isl_420352_Sint_Gillis_Waas_20200307_null_2":"background",
"epi_isl_420589_New_York_20200318_null_1":"background",
"epi_isl_420664_England_20200326_null_1":"background",
"epi_isl_420901_Munich_20200312_null_5":"background",
"epi_isl_421251_Jiangxi_20200203_null_5":"background",
"epi_isl_421510_Hauts_de_France_20200323_null_3":"background",
"epi_isl_421572_KZN_20200323_null_1":"background",
"epi_isl_421651_Taipei_20200322_null_1":"background",
"epi_isl_421654_Latvia_20200325_null_3":"background",
"epi_isl_422125_Wales_20200328_null_1":"background",
"epi_isl_422289_Wales_20200325_null_5":"background",
"epi_isl_422302_Wales_20200327_null_1":"background",
"epi_isl_422349_Wales_20200324_null_2":"background",
"epi_isl_422635_Zuid_Holland_20200331_null_1":"background",
"epi_isl_422774_Netherlands_20200327_null_5":"background",
"epi_isl_422905_Zuid_Holland_20200313_null_3":"background",
"epi_isl_422954_Zuid_Holland_20200327_null_27":"background",
"epi_isl_422964_Washington_20200316_null_1":"background",
"epi_isl_422977_Washington_20200317_null_3":"background",
"epi_isl_423033_Washington_20200318_null_6099":"background"
}
},
"timers":{
"MEME analysis":{
"order":2,
"timer":4
},
"Model fitting":{
"order":1,
"timer":2
},
"Total time":{
"order":0,
"timer":7
}
}
}