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[2.448184536534504, 0, 1, 1.388026545568758, 0, 0, 0.6666666666666666, 0, 0.009693038603686838, -10.12386038341112, -10.12386039387999],
[0, 0, 0.75, 0, 0.25, 0, 0.6666666666666666, 0, 0, -11.07435279560764, -11.07435279560764],
[2.20873340813516, 0, 1, 1.095182967545363, 0, 0, 0.6666666666666666, 0, 0.008744985466092607, -10.90630914663868, -10.90625402445544]
]
},
"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"
},
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"EBF site 121 (partition 1)":1,
"EBF site 124 (partition 1)":0.9999999949752406,
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"EBF site 13 (partition 1)":1,
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"EBF site 133 (partition 1)":1,
"EBF site 135 (partition 1)":1,
"EBF site 136 (partition 1)":1,
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"EBF site 146 (partition 1)":1,
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"EBF site 152 (partition 1)":1,
"EBF site 158 (partition 1)":1,
"EBF site 159 (partition 1)":1,
"EBF site 16 (partition 1)":1,
"EBF site 160 (partition 1)":1,
"EBF site 162 (partition 1)":1,
"EBF site 166 (partition 1)":1,
"EBF site 168 (partition 1)":1,
"EBF site 17 (partition 1)":1,
"EBF site 172 (partition 1)":1,
"EBF site 176 (partition 1)":1,
"EBF site 178 (partition 1)":1,
"EBF site 179 (partition 1)":1,
"EBF site 18 (partition 1)":1,
"EBF site 180 (partition 1)":1,
"EBF site 21 (partition 1)":1,
"EBF site 23 (partition 1)":1,
"EBF site 24 (partition 1)":1,
"EBF site 27 (partition 1)":1,
"EBF site 3 (partition 1)":1,
"EBF site 30 (partition 1)":1,
"EBF site 31 (partition 1)":1,
"EBF site 32 (partition 1)":1,
"EBF site 35 (partition 1)":1,
"EBF site 36 (partition 1)":1,
"EBF site 37 (partition 1)":1,
"EBF site 38 (partition 1)":1,
"EBF site 4 (partition 1)":1,
"EBF site 41 (partition 1)":1,
"EBF site 43 (partition 1)":1,
"EBF site 45 (partition 1)":1,
"EBF site 46 (partition 1)":1,
"EBF site 47 (partition 1)":1,
"EBF site 48 (partition 1)":1,
"EBF site 49 (partition 1)":0.9999999949752406,
"EBF site 5 (partition 1)":1,
"EBF site 56 (partition 1)":0.9999999949752406,
"EBF site 60 (partition 1)":1,
"EBF site 61 (partition 1)":1,
"EBF site 64 (partition 1)":1,
"EBF site 65 (partition 1)":1,
"EBF site 7 (partition 1)":1,
"EBF site 74 (partition 1)":1,
"EBF site 75 (partition 1)":1,
"EBF site 76 (partition 1)":1,
"EBF site 8 (partition 1)":1,
"EBF site 80 (partition 1)":1,
"EBF site 82 (partition 1)":1,
"EBF site 83 (partition 1)":1,
"EBF site 84 (partition 1)":1,
"EBF site 86 (partition 1)":1,
"EBF site 87 (partition 1)":1,
"EBF site 88 (partition 1)":1,
"EBF site 9 (partition 1)":1,
"EBF site 90 (partition 1)":1,
"EBF site 92 (partition 1)":1,
"EBF site 94 (partition 1)":1,
"EBF site 95 (partition 1)":1,
"EBF site 97 (partition 1)":1,
"EBF site 98 (partition 1)":1,
"EBF site 99 (partition 1)":1,
"Global MG94xREV":0,
"Nucleotide GTR":0.0009405282466589679
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"epi_isl_406595_Guandong_20200116_null_1":{
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},
"epi_isl_406799_Wuhan_20191231_null_1":{
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"epi_isl_408483_Shanghai_20200120_null_1":{
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"original name":"epi_isl_408483_Shanghai_20200120_null_1"
},
"epi_isl_413747_China_20200201_null_1":{
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"Nucleotide GTR":0.00209950875697024,
"original name":"epi_isl_413747_China_20200201_null_1"
},
"epi_isl_413752_China_20200201_null_1":{
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"Nucleotide GTR":0.002048515470392579,
"original name":"epi_isl_413752_China_20200201_null_1"
},
"epi_isl_413851_Guangdong_20200130_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"original name":"epi_isl_413851_Guangdong_20200130_null_1"
},
"epi_isl_414934_Shandong_20200121_null_1":{
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"Nucleotide GTR":0.001853864060935561,
"original name":"epi_isl_414934_Shandong_20200121_null_1"
},
"epi_isl_416650_USA_20200310_null_1":{
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"Nucleotide GTR":0.00185351096618514,
"original name":"epi_isl_416650_USA_20200310_null_1"
},
"epi_isl_416713_Washington_20200315_null_1":{
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"Nucleotide GTR":0.001854339601724577,
"original name":"epi_isl_416713_Washington_20200315_null_1"
},
"epi_isl_416726_Washington_20200313_null_1":{
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"original name":"epi_isl_416726_Washington_20200313_null_1"
},
"epi_isl_417067_Washington_20200303_null_1":{
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"Nucleotide GTR":0.001853915627106726,
"original name":"epi_isl_417067_Washington_20200303_null_1"
},
"epi_isl_417094_Washington_20200228_null_1":{
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"Nucleotide GTR":0.001853725170656441,
"original name":"epi_isl_417094_Washington_20200228_null_1"
},
"epi_isl_417347_Washington_20200312_null_1":{
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"Nucleotide GTR":0.001853638013270668,
"original name":"epi_isl_417347_Washington_20200312_null_1"
},
"epi_isl_417413_Turkey_20200317_null_1":{
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"Nucleotide GTR":0.003752319214416354,
"original name":"epi_isl_417413_Turkey_20200317_null_1"
},
"epi_isl_417798_Reykjavik_20200313_null_3":{
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"original name":"epi_isl_417798_Reykjavik_20200313_null_3"
},
"epi_isl_418768_England_20200318_null_1":{
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"Nucleotide GTR":0.001877037304792014,
"original name":"epi_isl_418768_England_20200318_null_1"
},
"epi_isl_418902_Minnesota_20200313_null_2":{
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"Nucleotide GTR":0.001853275557061237,
"original name":"epi_isl_418902_Minnesota_20200313_null_2"
},
"epi_isl_418989_Vorst_20200304_null_2":{
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"Nucleotide GTR":0.00185351096618514,
"original name":"epi_isl_418989_Vorst_20200304_null_2"
},
"epi_isl_419419_Wales_20200318_null_1":{
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"Nucleotide GTR":0.00185433960072635,
"original name":"epi_isl_419419_Wales_20200318_null_1"
},
"epi_isl_419442_Wales_20200318_null_1":{
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},
"epi_isl_419522_Connecticut_20200318_null_1":{
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"Nucleotide GTR":0.001853728169618241,
"original name":"epi_isl_419522_Connecticut_20200318_null_1"
},
"epi_isl_419847_Victoria_20200317_null_1":{
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"Nucleotide GTR":0.001855585115985694,
"original name":"epi_isl_419847_Victoria_20200317_null_1"
},
"epi_isl_419868_Victoria_20200318_null_1":{
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"Nucleotide GTR":0.001853725170495828,
"original name":"epi_isl_419868_Victoria_20200318_null_1"
},
"epi_isl_420310_Norway_20200316_null_2":{
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"Nucleotide GTR":0.001853321231539392,
"original name":"epi_isl_420310_Norway_20200316_null_2"
},
"epi_isl_420344_Havelange_20200305_null_1":{
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"Nucleotide GTR":0.001855315855581676,
"original name":"epi_isl_420344_Havelange_20200305_null_1"
},
"epi_isl_420617_ARA_20200323_null_2":{
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"Nucleotide GTR":0.001853169868162167,
"original name":"epi_isl_420617_ARA_20200323_null_2"
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"epi_isl_420942_Wales_20200321_null_1":{
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"Nucleotide GTR":0.001854187274887859,
"original name":"epi_isl_420942_Wales_20200321_null_1"
},
"epi_isl_421203_Li_ge_20200330_null_1":{
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"Nucleotide GTR":0.001855242169208674,
"original name":"epi_isl_421203_Li_ge_20200330_null_1"
},
"epi_isl_421248_Jiangxi_20200123_null_2":{
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"Nucleotide GTR":0.001853170543238597,
"original name":"epi_isl_421248_Jiangxi_20200123_null_2"
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"epi_isl_421335_Wisconsin_20200319_null_1":{
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"Nucleotide GTR":0.001854197701382101,
"original name":"epi_isl_421335_Wisconsin_20200319_null_1"
},
"epi_isl_421504_Ile_de_France_20200314_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"original name":"epi_isl_421504_Ile_de_France_20200314_null_1"
},
"epi_isl_421584_New_Jersey_20200318_null_1":{
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"Nucleotide GTR":0.001860996308898381,
"original name":"epi_isl_421584_New_Jersey_20200318_null_1"
},
"epi_isl_421668_India_20200310_null_3":{
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"Nucleotide GTR":0,
"original name":"epi_isl_421668_India_20200310_null_3"
},
"epi_isl_421893_England_20200327_null_1":{
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"Nucleotide GTR":0.001853929954489813,
"original name":"epi_isl_421893_England_20200327_null_1"
},
"epi_isl_421969_England_20200401_null_5":{
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"Nucleotide GTR":0.001853170541718967,
"original name":"epi_isl_421969_England_20200401_null_5"
},
"epi_isl_422000_England_20200402_null_1":{
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"Nucleotide GTR":0.001854241373833567,
"original name":"epi_isl_422000_England_20200402_null_1"
},
"epi_isl_422062_Wales_20200330_null_1":{
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"Nucleotide GTR":0.001854016224058782,
"original name":"epi_isl_422062_Wales_20200330_null_1"
},
"epi_isl_422072_Wales_20200328_null_1":{
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"Nucleotide GTR":0.001854261136007963,
"original name":"epi_isl_422072_Wales_20200328_null_1"
},
"epi_isl_422092_Wales_20200327_null_1":{
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"Nucleotide GTR":0,
"original name":"epi_isl_422092_Wales_20200327_null_1"
},
"epi_isl_422295_Wales_20200325_null_1":{
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"Nucleotide GTR":0.001854318807694896,
"original name":"epi_isl_422295_Wales_20200325_null_1"
},
"epi_isl_422346_Wales_20200326_null_1":{
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"Nucleotide GTR":0.000912924582919264,
"original name":"epi_isl_422346_Wales_20200326_null_1"
},
"epi_isl_422347_Wales_20200325_null_1":{
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"Nucleotide GTR":0.001853573541593455,
"original name":"epi_isl_422347_Wales_20200325_null_1"
},
"epi_isl_422357_Wales_20200327_null_1":{
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"Nucleotide GTR":0.001853817985983461,
"original name":"epi_isl_422357_Wales_20200327_null_1"
},
"epi_isl_422359_Wales_20200324_null_1":{
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"Nucleotide GTR":0.001853293983901594,
"original name":"epi_isl_422359_Wales_20200324_null_1"
},
"epi_isl_422397_Greater_Accra_20200329_null_2":{
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"Nucleotide GTR":0.001853170543238597,
"original name":"epi_isl_422397_Greater_Accra_20200329_null_2"
},
"epi_isl_422418_Taipei_20200319_null_1":{
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"Nucleotide GTR":0.001854619395134467,
"original name":"epi_isl_422418_Taipei_20200319_null_1"
},
"epi_isl_422547_New_York_20200320_null_1":{
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"Nucleotide GTR":0.001853573550815342,
"original name":"epi_isl_422547_New_York_20200320_null_1"
},
"epi_isl_422793_Netherlands_20200330_null_1":{
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"Nucleotide GTR":0.001853817059315328,
"original name":"epi_isl_422793_Netherlands_20200330_null_1"
},
"epi_isl_422885_Noord_Brabant_20200324_null_3":{
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"Nucleotide GTR":0.001860761555513909,
"original name":"epi_isl_422885_Noord_Brabant_20200324_null_3"
},
"epi_isl_422888_Noord_Brabant_20200317_null_1":{
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"Nucleotide GTR":0.00185501466551438,
"original name":"epi_isl_422888_Noord_Brabant_20200317_null_1"
},
"epi_isl_422904_Zuid_Holland_20200309_null_1":{
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"Nucleotide GTR":0.003710436941268133,
"original name":"epi_isl_422904_Zuid_Holland_20200309_null_1"
},
"epi_isl_422919_Zuid_Holland_20200319_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"original name":"epi_isl_422919_Zuid_Holland_20200319_null_1"
},
"epi_isl_422961_Illinois_20200313_null_1":{
"Global MG94xREV":0.001864268601097478,
"Nucleotide GTR":0.001854004217503738,
"original name":"epi_isl_422961_Illinois_20200313_null_1"
},
"epi_isl_423012_Washington_20200319_null_1":{
"Global MG94xREV":0.003734510643216976,
"Nucleotide GTR":0.003715419020076238,
"original name":"epi_isl_423012_Washington_20200319_null_1"
},
"epi_isl_423295_England_20200326_null_2":{
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"Nucleotide GTR":0.001853685561816378,
"original name":"epi_isl_423295_England_20200326_null_2"
},
"epi_isl_423369_England_20200329_null_3":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"original name":"epi_isl_423369_England_20200329_null_3"
},
"epi_isl_423388_England_20200330_null_1":{
"Global MG94xREV":0.001865898448069458,
"Nucleotide GTR":0.001854379965207303,
"original name":"epi_isl_423388_England_20200330_null_1"
},
"epi_isl_423459_England_20200330_null_1":{
"Global MG94xREV":0.001864239914787472,
"Nucleotide GTR":0.001854688406410477,
"original name":"epi_isl_423459_England_20200330_null_1"
},
"epi_isl_423762_England_20200324_null_3":{
"Global MG94xREV":0.001864725696918866,
"Nucleotide GTR":0.001853573541542157,
"original name":"epi_isl_423762_England_20200324_null_3"
},
"epi_isl_423813_England_20200323_null_4":{
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"Nucleotide GTR":0.001854722541936071,
"original name":"epi_isl_423813_England_20200323_null_4"
},
"epi_isl_423844_England_20200323_null_1":{
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"Nucleotide GTR":0.001853915628518188,
"original name":"epi_isl_423844_England_20200323_null_1"
},
"epi_isl_424096_England_20200311_null_1":{
"Global MG94xREV":0.001864279956080164,
"Nucleotide GTR":0.001853810913817062,
"original name":"epi_isl_424096_England_20200311_null_1"
},
"epi_isl_424131_England_20200321_null_4":{
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"Nucleotide GTR":0.001853573072821122,
"original name":"epi_isl_424131_England_20200321_null_4"
},
"epi_isl_424146_England_20200321_null_1":{
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"Nucleotide GTR":0.001852422529918554,
"original name":"epi_isl_424146_England_20200321_null_1"
},
"epi_isl_424148_England_20200320_null_1":{
"Global MG94xREV":0.001864231306918542,
"Nucleotide GTR":0.001854119869071156,
"original name":"epi_isl_424148_England_20200320_null_1"
},
"epi_isl_424214_Washington_20200320_null_1":{
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"Nucleotide GTR":0.001853432527826236,
"original name":"epi_isl_424214_Washington_20200320_null_1"
},
"epi_isl_424301_Washington_20200324_null_4":{
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"Nucleotide GTR":0.003736952659593304,
"original name":"epi_isl_424301_Washington_20200324_null_4"
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"epi_isl_424352_Anhui_20200310_null_2":{
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"Nucleotide GTR":0.001854559077581263,
"original name":"epi_isl_424352_Anhui_20200310_null_2"
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"epi_isl_424451_Reykjavik_20200320_null_1":{
"Global MG94xREV":0.001865785140709053,
"Nucleotide GTR":0.001854067618900478,
"original name":"epi_isl_424451_Reykjavik_20200320_null_1"
},
"epi_isl_424485_Reykjavik_20200320_null_4":{
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"Nucleotide GTR":0.001854163092135373,
"original name":"epi_isl_424485_Reykjavik_20200320_null_4"
},
"epi_isl_424518_Reykjavik_20200321_null_1":{
"Global MG94xREV":0.001865061575750973,
"Nucleotide GTR":0.001853573072821122,
"original name":"epi_isl_424518_Reykjavik_20200321_null_1"
},
"epi_isl_424650_Li_ge_20200404_null_7":{
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"Nucleotide GTR":0.001853816978691134,
"original name":"epi_isl_424650_Li_ge_20200404_null_7"
},
"epi_isl_424907_Virginia_20200306_null_4":{
"Global MG94xREV":0.001863160244127003,
"Nucleotide GTR":0.001854016139134747,
"original name":"epi_isl_424907_Virginia_20200306_null_4"
},
"epi_isl_425218_Comunitat_Valenciana_20200317_null_2":{
"Global MG94xREV":0.001864064698907342,
"Nucleotide GTR":0.00185317046138665,
"original name":"epi_isl_425218_Comunitat_Valenciana_20200317_null_2"
},
"epi_isl_425241_England_20200401_null_1":{
"Global MG94xREV":0.001864693293611773,
"Nucleotide GTR":0.001853725170691597,
"original name":"epi_isl_425241_England_20200401_null_1"
},
"epi_isl_425281_England_20200330_null_1":{
"Global MG94xREV":0.001863510499853404,
"Nucleotide GTR":0.001853170541718967,
"original name":"epi_isl_425281_England_20200330_null_1"
},
"epi_isl_425293_England_20200319_null_3":{
"Global MG94xREV":0.001862756696504339,
"Nucleotide GTR":0.001852480009727365,
"original name":"epi_isl_425293_England_20200319_null_3"
},
"epi_isl_425302_England_20200327_null_3":{
"Global MG94xREV":0.001863643163062294,
"Nucleotide GTR":0.001854219698565145,
"original name":"epi_isl_425302_England_20200327_null_3"
},
"epi_isl_425413_England_20200316_null_3":{
"Global MG94xREV":0.001862520305363427,
"Nucleotide GTR":0.001821437573151067,
"original name":"epi_isl_425413_England_20200316_null_3"
},
"epi_isl_425420_England_20200316_null_1":{
"Global MG94xREV":0.001863447755429769,
"Nucleotide GTR":0.001853413928490672,
"original name":"epi_isl_425420_England_20200316_null_1"
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"epi_isl_425430_England_20200330_null_1":{
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"epi_isl_425512_England_20200319_null_16":{
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"epi_isl_425625_England_20200328_null_30":{
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"epi_isl_425694_Scotland_20200317_null_3":{
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"epi_isl_426427_Minnesota_20200307_null_179":{
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"epi_isl_426628_Louisiana_20200406_null_5":{
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},
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"epi_isl_426930_Victoria_20200328_null_1":{
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"epi_isl_426956_Victoria_20200328_null_1":{
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"epi_isl_427053_Victoria_20200331_null_1":{
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"epi_isl_427098_Victoria_20200404_null_1":{
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"epi_isl_427099_Victoria_20200404_null_1":{
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},
"epi_isl_427104_Victoria_20200404_null_1":{
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"epi_isl_427154_Victoria_20200328_null_2":{
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"epi_isl_427212_Washington_20200327_null_18":{
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"epi_isl_427264_Washington_20200329_null_1":{
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"epi_isl_427271_Arizona_20200323_null_76":{
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"epi_isl_427288_OHIO_20200331_null_71":{
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"epi_isl_427303_Rio_de_Janeiro_20200325_null_1":{
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"original name":"epi_isl_427303_Rio_de_Janeiro_20200325_null_1"
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"epi_isl_427306_Santa_Catarina_20200310_null_9026":{
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"original name":"epi_isl_427306_Santa_Catarina_20200310_null_9026"
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"epi_isl_427351_Liege_20200407_null_16":{
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"attributes":{
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"display order":3
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"EBF site 100 (partition 1)":{
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"EBF site 101 (partition 1)":{
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"EBF site 103 (partition 1)":{
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"EBF site 104 (partition 1)":{
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"EBF site 105 (partition 1)":{
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"EBF site 106 (partition 1)":{
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"EBF site 107 (partition 1)":{
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"EBF site 110 (partition 1)":{
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"EBF site 111 (partition 1)":{
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"EBF site 114 (partition 1)":{
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"EBF site 115 (partition 1)":{
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"EBF site 117 (partition 1)":{
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"EBF site 118 (partition 1)":{
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"EBF site 119 (partition 1)":{
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"EBF site 12 (partition 1)":{
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"EBF site 120 (partition 1)":{
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"EBF site 121 (partition 1)":{
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"EBF site 124 (partition 1)":{
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"EBF site 127 (partition 1)":{
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"EBF site 129 (partition 1)":{
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"display order":131
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"EBF site 13 (partition 1)":{
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"EBF site 131 (partition 1)":{
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"EBF site 132 (partition 1)":{
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"EBF site 133 (partition 1)":{
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"EBF site 135 (partition 1)":{
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"EBF site 136 (partition 1)":{
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"EBF site 137 (partition 1)":{
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"EBF site 138 (partition 1)":{
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"EBF site 139 (partition 1)":{
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"EBF site 140 (partition 1)":{
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"EBF site 144 (partition 1)":{
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"display order":146
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"EBF site 145 (partition 1)":{
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"display order":147
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"EBF site 146 (partition 1)":{
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"display order":148
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"EBF site 148 (partition 1)":{
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"EBF site 152 (partition 1)":{
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"EBF site 158 (partition 1)":{
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"display order":160
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"EBF site 159 (partition 1)":{
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"display order":161
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"EBF site 16 (partition 1)":{
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"EBF site 160 (partition 1)":{
"attribute type":"branch label",
"display order":162
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"EBF site 162 (partition 1)":{
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"EBF site 166 (partition 1)":{
"attribute type":"branch label",
"display order":168
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"EBF site 168 (partition 1)":{
"attribute type":"branch label",
"display order":170
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"EBF site 17 (partition 1)":{
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"display order":19
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"EBF site 172 (partition 1)":{
"attribute type":"branch label",
"display order":174
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"EBF site 176 (partition 1)":{
"attribute type":"branch label",
"display order":178
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"EBF site 178 (partition 1)":{
"attribute type":"branch label",
"display order":180
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"EBF site 179 (partition 1)":{
"attribute type":"branch label",
"display order":181
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"EBF site 18 (partition 1)":{
"attribute type":"branch label",
"display order":20
},
"EBF site 180 (partition 1)":{
"attribute type":"branch label",
"display order":182
},
"EBF site 21 (partition 1)":{
"attribute type":"branch label",
"display order":23
},
"EBF site 23 (partition 1)":{
"attribute type":"branch label",
"display order":25
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"EBF site 24 (partition 1)":{
"attribute type":"branch label",
"display order":26
},
"EBF site 27 (partition 1)":{
"attribute type":"branch label",
"display order":29
},
"EBF site 3 (partition 1)":{
"attribute type":"branch label",
"display order":5
},
"EBF site 30 (partition 1)":{
"attribute type":"branch label",
"display order":32
},
"EBF site 31 (partition 1)":{
"attribute type":"branch label",
"display order":33
},
"EBF site 32 (partition 1)":{
"attribute type":"branch label",
"display order":34
},
"EBF site 35 (partition 1)":{
"attribute type":"branch label",
"display order":37
},
"EBF site 36 (partition 1)":{
"attribute type":"branch label",
"display order":38
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"EBF site 37 (partition 1)":{
"attribute type":"branch label",
"display order":39
},
"EBF site 38 (partition 1)":{
"attribute type":"branch label",
"display order":40
},
"EBF site 4 (partition 1)":{
"attribute type":"branch label",
"display order":6
},
"EBF site 41 (partition 1)":{
"attribute type":"branch label",
"display order":43
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"EBF site 43 (partition 1)":{
"attribute type":"branch label",
"display order":45
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"EBF site 45 (partition 1)":{
"attribute type":"branch label",
"display order":47
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"EBF site 46 (partition 1)":{
"attribute type":"branch label",
"display order":48
},
"EBF site 47 (partition 1)":{
"attribute type":"branch label",
"display order":49
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"EBF site 48 (partition 1)":{
"attribute type":"branch label",
"display order":50
},
"EBF site 49 (partition 1)":{
"attribute type":"branch label",
"display order":51
},
"EBF site 5 (partition 1)":{
"attribute type":"branch label",
"display order":7
},
"EBF site 56 (partition 1)":{
"attribute type":"branch label",
"display order":58
},
"EBF site 60 (partition 1)":{
"attribute type":"branch label",
"display order":62
},
"EBF site 61 (partition 1)":{
"attribute type":"branch label",
"display order":63
},
"EBF site 64 (partition 1)":{
"attribute type":"branch label",
"display order":66
},
"EBF site 65 (partition 1)":{
"attribute type":"branch label",
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"EBF site 7 (partition 1)":{
"attribute type":"branch label",
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"EBF site 74 (partition 1)":{
"attribute type":"branch label",
"display order":76
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"EBF site 75 (partition 1)":{
"attribute type":"branch label",
"display order":77
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"EBF site 76 (partition 1)":{
"attribute type":"branch label",
"display order":78
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"EBF site 8 (partition 1)":{
"attribute type":"branch label",
"display order":10
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"EBF site 80 (partition 1)":{
"attribute type":"branch label",
"display order":82
},
"EBF site 82 (partition 1)":{
"attribute type":"branch label",
"display order":84
},
"EBF site 83 (partition 1)":{
"attribute type":"branch label",
"display order":85
},
"EBF site 84 (partition 1)":{
"attribute type":"branch label",
"display order":86
},
"EBF site 86 (partition 1)":{
"attribute type":"branch label",
"display order":88
},
"EBF site 87 (partition 1)":{
"attribute type":"branch label",
"display order":89
},
"EBF site 88 (partition 1)":{
"attribute type":"branch label",
"display order":90
},
"EBF site 9 (partition 1)":{
"attribute type":"branch label",
"display order":11
},
"EBF site 90 (partition 1)":{
"attribute type":"branch label",
"display order":92
},
"EBF site 92 (partition 1)":{
"attribute type":"branch label",
"display order":94
},
"EBF site 94 (partition 1)":{
"attribute type":"branch label",
"display order":96
},
"EBF site 95 (partition 1)":{
"attribute type":"branch label",
"display order":97
},
"EBF site 97 (partition 1)":{
"attribute type":"branch label",
"display order":99
},
"EBF site 98 (partition 1)":{
"attribute type":"branch label",
"display order":100
},
"EBF site 99 (partition 1)":{
"attribute type":"branch label",
"display order":101
},
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"original name":{
"attribute type":"node label",
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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, 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, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179]
],
"name":"meme.filter.default"
}
},
"fits":{
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"Equilibrium frequencies": [
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[0.01733724410192433],
[0.0122791527078038],
[0.02745315003536972],
[0.03517613075229757],
[0.03471044320683725],
[0.02458377064928089],
[0.05496323403820074],
[0.01414855353363561],
[0.01396124455376828],
[0.009888091374781232],
[0.02210732796757168],
[0.02246083314850519],
[0.02216348008453188],
[0.01569734814220723],
[0.03509539004524066],
[0.02880301498473926],
[0.0284216994431138],
[0.0201297498971339],
[0.04500514467494765],
[0.01235168293437126],
[0.01955862205048913],
[0.005034751247227558],
[0.004968097499354177],
[0.003518669259265781],
[0.007866874645029475],
[0.007886856330099104],
[0.005585888546787366],
[0.01248866595317671],
[0.01024952941469111],
[0.01011383858988545],
[0.007163155099921459],
[0.0160150440640574]
],
"Log Likelihood":-1794.458697707338,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *background*": [
[0.6073643343141918, 1]
],
"non-synonymous/synonymous rate ratio for *test*": [
[0.3775487343024745, 1]
]
},
"display order":1,
"estimated parameters":162
},
"Nucleotide GTR":{
"AIC-c":4200.737539719516,
"Equilibrium frequencies": [
[0.2503272769122322],
[0.2145066390459339],
[0.2699063484528074],
[0.2652597355890264]
],
"Log Likelihood":-1836.368251097869,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.09642778307920973,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.3927071365269911,
"Substitution rate from nucleotide C to nucleotide G":0.05886098542402236,
"Substitution rate from nucleotide C to nucleotide T":1.613620785389765,
"Substitution rate from nucleotide G to nucleotide T":0.6286448015848439
},
"display order":0,
"estimated parameters":263
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-04-18/sequences.leader.compressed.fas",
"number of sequences":129,
"number of sites":180,
"partition count":1,
"trees":{
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_Noord_Brabant_20200324_null_3,epi_isl_424650_Li_ge_20200404_null_7,epi_isl_426749_Victoria_20200325_null_1,epi_isl_417798_Reykjavik_20200313_null_3,epi_isl_427212_Washington_20200327_null_18,(epi_isl_413747_China_20200201_null_1,epi_isl_422346_Wales_20200326_null_1)Node91,epi_isl_423459_England_20200330_null_1)"
}
},
"tested":{
"0":{
"Node108":"test",
"Node132":"test",
"Node136":"test",
"Node139":"test",
"Node144":"test",
"Node145":"test",
"Node148":"test",
"Node153":"test",
"Node190":"test",
"Node2":"test",
"Node203":"test",
"Node219":"test",
"Node250":"test",
"Node50":"test",
"Node57":"test",
"Node70":"test",
"Node91":"test",
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"epi_isl_408483_Shanghai_20200120_null_1":"background",
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"epi_isl_416726_Washington_20200313_null_1":"background",
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"epi_isl_417094_Washington_20200228_null_1":"background",
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"epi_isl_418768_England_20200318_null_1":"background",
"epi_isl_418902_Minnesota_20200313_null_2":"background",
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"epi_isl_427212_Washington_20200327_null_18":"background",
"epi_isl_427218_Washington_20200327_null_3":"background",
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"epi_isl_427271_Arizona_20200323_null_76":"background",
"epi_isl_427288_OHIO_20200331_null_71":"background",
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"epi_isl_427306_Santa_Catarina_20200310_null_9026":"background",
"epi_isl_427351_Liege_20200407_null_16":"background"
}
},
"timers":{
"MEME analysis":{
"order":2,
"timer":33
},
"Model fitting":{
"order":1,
"timer":22
},
"Total time":{
"order":0,
"timer":56
}
}
}