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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":0.009423671318655328,
"Nucleotide GTR":0.008843567266216733,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "M", "-", "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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],
"nonsynonymous substitution count": [
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],
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]
},
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"Nucleotide GTR":0.06552244535045401,
"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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],
"nonsynonymous substitution count": [
[1.5, 1.5, 2, 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]
],
"synonymous substitution count": [
[0.5, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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":0.008782910954895745,
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],
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],
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],
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]
},
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"Nucleotide GTR":0.0007456560308669853,
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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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"Global MG94xREV":3.064249345880125,
"Nucleotide GTR":2.875619734010237,
"amino-acid": [
["-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "F", "Y", "N", "-", "-", "V", "K", "V", "I", "L", "I", "V", "L", "F", "L", "G", "-", "-", "-", "-", "-"]
],
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],
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],
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]
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"Nucleotide GTR":0.2817737247379191,
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],
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],
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"Nucleotide GTR":0.4699836807044895,
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],
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"Nucleotide GTR":0.005482839560286448,
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"Nucleotide GTR":0.008853950751369211,
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"Nucleotide GTR":0.006769669487054148,
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"Nucleotide GTR":0.006753944618623191,
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"Nucleotide GTR":0.008782820715428316,
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"epi_isl_414480_USA_20200221_null_1":{
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.008818478759604589,
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"Nucleotide GTR":1.871008378695934,
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"epi_isl_415435_Wales_20200306_null_1":{
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
"amino-acid": [
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"Nucleotide GTR":0.01092405572644593,
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"codon": [
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"Nucleotide GTR":0.008840528397966004,
"amino-acid": [
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"Nucleotide GTR":0.03263005665049265,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.008780644553250255,
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"Nucleotide GTR":0.008790083270366986,
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"amino-acid": [
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"Global MG94xREV":0.3656734619803803,
"Nucleotide GTR":0.3431632692973938,
"amino-acid": [
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"Nucleotide GTR":0.008843187471195059,
"amino-acid": [
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"Global MG94xREV":1.474708530161651,
"Nucleotide GTR":1.383928157461364,
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"epi_isl_424600_Reykjavik_20200327_null_1":{
"Global MG94xREV":0.00935730888797919,
"Nucleotide GTR":0.008781289985973287,
"amino-acid": [
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"original name":"epi_isl_424600_Reykjavik_20200327_null_1",
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"Global MG94xREV":0.009369376535220113,
"Nucleotide GTR":0.008792614770816821,
"amino-acid": [
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"Nucleotide GTR":0.2104189832036934,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_426103_Washington_20200323_null_2",
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"epi_isl_426949_Victoria_20200328_null_1":{
"Global MG94xREV":0.009433030090486507,
"Nucleotide GTR":0.008852349929089775,
"amino-acid": [
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"original name":"epi_isl_426949_Victoria_20200328_null_1",
"synonymous substitution count": [
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"epi_isl_427272_Arizona_20200323_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_427272_Arizona_20200323_null_3",
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"epi_isl_428685_Madrid_20200327_null_1":{
"Global MG94xREV":2.006732872386124,
"Nucleotide GTR":1.883202049624041,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_428685_Madrid_20200327_null_1",
"synonymous substitution count": [
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"epi_isl_429464_Unknown_20200323_null_1":{
"Global MG94xREV":0.009366697374018048,
"Nucleotide GTR":0.008790100533901481,
"amino-acid": [
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"original name":"epi_isl_429464_Unknown_20200323_null_1",
"synonymous substitution count": [
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"epi_isl_429689_Minas_gerais_20200317_null_1":{
"Global MG94xREV":0.01830594957850736,
"Nucleotide GTR":0.01717906864483066,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_429689_Minas_gerais_20200317_null_1",
"synonymous substitution count": [
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"epi_isl_430520_Victoria_20200402_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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"synonymous substitution count": [
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"epi_isl_430566_Victoria_20200406_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"epi_isl_430608_Victoria_20200408_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"Nucleotide GTR":0,
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"Nucleotide GTR":0.002120153715054012,
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"Nucleotide GTR":0.4295532484030303,
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"epi_isl_430903_USA_20200405_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_430903_USA_20200405_null_3",
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"Nucleotide GTR":0,
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"epi_isl_432289_Wales_20200401_null_1":{
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"Nucleotide GTR":0,
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"epi_isl_432401_Wales_20200330_null_1":{
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"Nucleotide GTR":0.008875468184095322,
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"epi_isl_432653_England_20200318_null_1":{
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"Nucleotide GTR":0,
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"epi_isl_433319_Scotland_20200325_null_1":{
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"Nucleotide GTR":0.008856783448076279,
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"epi_isl_433486_England_20200417_null_1":{
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"Nucleotide GTR":0.008857272236806065,
"amino-acid": [
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"epi_isl_433657_Scotland_20200405_null_1":{
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"Nucleotide GTR":0.008855759521142918,
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"epi_isl_433714_England_20200405_null_1":{
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"Nucleotide GTR":0.00895158167174271,
"amino-acid": [
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"epi_isl_434251_Washington_20200402_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_434332_Washington_20200326_null_1":{
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"Nucleotide GTR":0.008791327702554447,
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"Nucleotide GTR":0.008988410838267574,
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"Nucleotide GTR":0,
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"Nucleotide GTR":0,
"amino-acid": [
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"Global MG94xREV":0.3818513532143289,
"Nucleotide GTR":0.3583452789956452,
"amino-acid": [
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]
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"epi_isl_437869_Connecticut_20200403_null_11":{
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"Nucleotide GTR":0,
"amino-acid": [
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"Global MG94xREV":0.009369637947122131,
"Nucleotide GTR":0.008792860090678003,
"amino-acid": [
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"original name":"epi_isl_438253_England_20200404_null_2",
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"epi_isl_438401_England_20200329_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_438977_Scotland_20200420_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_439881_England_20200323_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"original name":"epi_isl_439881_England_20200323_null_1",
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"epi_isl_440074_England_20200323_null_3":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_440074_England_20200323_null_3",
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"epi_isl_440493_England_20200310_null_4":{
"Global MG94xREV":0.009437713498828331,
"Nucleotide GTR":0.008856745035339311,
"amino-acid": [
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"codon": [
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"epi_isl_440730_England_20200402_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_441602_England_20200406_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
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"epi_isl_442012_England_20200324_null_3":{
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"Nucleotide GTR":0.002077139499089521,
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]
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"epi_isl_442129_England_20200407_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "P", "F", "T", "-", "I", "YC", "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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"original name":"epi_isl_442129_England_20200407_null_1",
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]
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"epi_isl_442145_England_20200405_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_442145_England_20200405_null_1",
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]
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"epi_isl_442883_England_20200410_null_1":{
"Global MG94xREV":0.009366935080997792,
"Nucleotide GTR":0.008790323608072255,
"amino-acid": [
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"original name":"epi_isl_442883_England_20200410_null_1",
"synonymous substitution count": [
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"epi_isl_443363_England_20200414_null_2":{
"Global MG94xREV":0.009444363007704413,
"Nucleotide GTR":0.008862985212553097,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_443363_England_20200414_null_2",
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]
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"epi_isl_443597_England_20200414_null_1":{
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"Nucleotide GTR":0,
"amino-acid": [
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"codon": [
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"original name":"epi_isl_443597_England_20200414_null_1",
"synonymous substitution count": [
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"epi_isl_443691_England_20200330_null_2":{
"Global MG94xREV":0.009433402943009794,
"Nucleotide GTR":0.008852699829490447,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_443691_England_20200330_null_2",
"synonymous substitution count": [
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]
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"epi_isl_444065_California_20200430_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_444065_California_20200430_null_1",
"synonymous substitution count": [
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]
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"epi_isl_444149_England_20200409_null_4":{
"Global MG94xREV":0.002137579018220093,
"Nucleotide GTR":0.00200599354490011,
"amino-acid": [
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"codon": [
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],
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"original name":"epi_isl_444149_England_20200409_null_4",
"synonymous substitution count": [
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]
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"epi_isl_444822_Unknown_20200311_null_6":{
"Global MG94xREV":0.001768918070771373,
"Nucleotide GTR":0.001660026694301681,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_444822_Unknown_20200311_null_6",
"synonymous substitution count": [
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]
},
"epi_isl_445873_Wales_20200408_null_2":{
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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_445873_Wales_20200408_null_2",
"synonymous substitution count": [
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]
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"epi_isl_446256_Wales_20200417_null_2":{
"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_446256_Wales_20200417_null_2",
"synonymous substitution count": [
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]
},
"epi_isl_446888_Wales_20200417_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_446888_Wales_20200417_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_446927_Wales_20200417_null_17":{
"Global MG94xREV":0.00936955773995737,
"Nucleotide GTR":0.008792784820920318,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_446927_Wales_20200417_null_17",
"synonymous substitution count": [
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]
},
"epi_isl_447015_Bangkok_20200331_null_6":{
"Global MG94xREV":0.008769381251894569,
"Nucleotide GTR":0.008229554104959546,
"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", "F", "T", "-", "-", "-", "-", "-"]
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"codon": [
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],
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],
"original name":"epi_isl_447015_Bangkok_20200331_null_6",
"synonymous substitution count": [
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]
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"epi_isl_447517_Comunitat_Valenciana_20200401_null_3":{
"Global MG94xREV":0.009436440881998248,
"Nucleotide GTR":0.008855550758484749,
"amino-acid": [
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],
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],
"original name":"epi_isl_447517_Comunitat_Valenciana_20200401_null_3",
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]
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"epi_isl_447596_Kinshasa_20200405_null_10":{
"Global MG94xREV":0.003026960958995105,
"Nucleotide GTR":0.002840626752345693,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_447596_Kinshasa_20200405_null_10",
"synonymous substitution count": [
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]
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"epi_isl_447617_Taipei_20200325_null_4":{
"Global MG94xREV":0.009438158769377345,
"Nucleotide GTR":0.008857162895843852,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_447617_Taipei_20200325_null_4",
"synonymous substitution count": [
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]
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"epi_isl_448167_Scotland_20200411_null_4":{
"Global MG94xREV":0.009437957237532754,
"Nucleotide GTR":0.008856973769932776,
"amino-acid": [
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"codon": [
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],
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],
"original name":"epi_isl_448167_Scotland_20200411_null_4",
"synonymous substitution count": [
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]
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"epi_isl_448447_England_20200427_null_1":{
"Global MG94xREV":0.008675972235252103,
"Nucleotide GTR":0.008141895177348882,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_448447_England_20200427_null_1",
"synonymous substitution count": [
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]
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"epi_isl_448730_England_20200101_null_24":{
"Global MG94xREV":0.003562837756767526,
"Nucleotide GTR":0.003343515949905421,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_448730_England_20200101_null_24",
"synonymous substitution count": [
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]
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"epi_isl_448967_Northern_Ireland_20200328_null_30":{
"Global MG94xREV":0.002247700045195221,
"Nucleotide GTR":0.002109335721908294,
"amino-acid": [
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_448967_Northern_Ireland_20200328_null_30",
"synonymous substitution count": [
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]
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"epi_isl_449194_Scotland_20200422_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "G", "Y", "I", "N", "V", "F", "A", "F", "PL", "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_449194_Scotland_20200422_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_449262_Scotland_20200503_null_1":{
"Global MG94xREV":0.009435589475814575,
"Nucleotide GTR":0.008854751763315918,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_449262_Scotland_20200503_null_1",
"synonymous substitution count": [
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]
},
"epi_isl_449302_Scotland_20200426_null_14":{
"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", "V", "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_449302_Scotland_20200426_null_14",
"synonymous substitution count": [
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]
},
"epi_isl_449493_England_20200324_null_20":{
"Global MG94xREV":0.009422934179015132,
"Nucleotide GTR":0.008842875503550979,
"amino-acid": [
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],
"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_449493_England_20200324_null_20",
"synonymous substitution count": [
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]
},
"epi_isl_449707_England_20200416_null_3":{
"Global MG94xREV":0.002964336948036666,
"Nucleotide GTR":0.002781857761507172,
"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", "I", "-", "-", "-", "-", "-"]
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"codon": [
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],
"nonsynonymous substitution count": [
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],
"original name":"epi_isl_449707_England_20200416_null_3",
"synonymous substitution count": [
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]
},
"epi_isl_449727_England_20200417_null_3":{
"Global MG94xREV":0.009367599245734375,
"Nucleotide GTR":0.008790946888036623,
"amino-acid": [
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"Global MG94xREV":0.009422535818048869,
"Nucleotide GTR":0.008842501664960652,
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"Nucleotide GTR":0.008843287667189031,
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"Nucleotide GTR":0.008803494198878537,
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"epi_isl_450721_Wisconsin_20200401_null_28229":{
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"Nucleotide GTR":0,
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"attributes":{
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"display order":1
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"Nucleotide GTR":{
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"original name":{
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"synonymous substitution count":{
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"data partitions":{
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"coverage": [
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],
"name":"slac.filter.default"
}
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"fits":{
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[0.02966400946956573],
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[0.04681789220007829]
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"Log Likelihood":-inf,
"Rate Distributions":{
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[0.9165418920175951, 1]
],
"non-synonymous/synonymous rate ratio for *test*": [
[0.9165418920175951, 1]
]
},
"display order":1,
"estimated parameters":146
},
"Nucleotide GTR":{
"AIC-c":2016.408275309444,
"Equilibrium frequencies": [
[0.2991317671092952],
[0.1828907048008171],
[0.1589376915219612],
[0.3590398365679264]
],
"Log Likelihood":-795.8926845085018,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.21177237992541,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.09210642612479583,
"Substitution rate from nucleotide C to nucleotide G":0.5730451696928873,
"Substitution rate from nucleotide C to nucleotide T":1.636576338061631,
"Substitution rate from nucleotide G to nucleotide T":0.6906141481737251
},
"display order":0,
"estimated parameters":209
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-22/sequences.ORF10.compressed.fas",
"number of sequences":102,
"number of sites":44,
"partition count":1,
"trees":{
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}
},
"tested":{
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"Node105":"test",
"Node118":"test",
"Node126":"test",
"Node127":"test",
"Node128":"test",
"Node129":"test",
"Node136":"test",
"Node137":"test",
"Node138":"test",
"Node148":"test",
"Node149":"test",
"Node161":"test",
"Node168":"test",
"Node176":"test",
"Node179":"test",
"Node183":"test",
"Node186":"test",
"Node194":"test",
"Node197":"test",
"Node21":"test",
"Node22":"test",
"Node44":"test",
"Node49":"test",
"Node50":"test",
"Node57":"test",
"Node63":"test",
"Node77":"test",
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"epi_isl_421889_England_20200327_null_1":"background",
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"epi_isl_422206_Wales_20200330_null_1":"background",
"epi_isl_422425_Zhejiang_20200124_null_1":"background",
"epi_isl_422636_Prague_20200308_null_1":"background",
"epi_isl_422985_Washington_20200317_null_1":"background",
"epi_isl_423536_England_20200331_null_1":"background",
"epi_isl_423770_England_20200322_null_1":"background",
"epi_isl_423904_England_20200318_null_1":"background",
"epi_isl_424158_England_20200321_null_1":"background",
"epi_isl_424288_Washington_20200322_null_1":"background",
"epi_isl_424315_Idaho_20200320_null_1":"background",
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"epi_isl_424600_Reykjavik_20200327_null_1":"background",
"epi_isl_425251_England_20200331_null_1":"background",
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"epi_isl_426949_Victoria_20200328_null_1":"background",
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"epi_isl_430520_Victoria_20200402_null_1":"background",
"epi_isl_430566_Victoria_20200406_null_1":"background",
"epi_isl_430608_Victoria_20200408_null_1":"background",
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"epi_isl_448167_Scotland_20200411_null_4":"background",
"epi_isl_448447_England_20200427_null_1":"background",
"epi_isl_448730_England_20200101_null_24":"background",
"epi_isl_448967_Northern_Ireland_20200328_null_30":"background",
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"epi_isl_449302_Scotland_20200426_null_14":"background",
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"epi_isl_449707_England_20200416_null_3":"background",
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"epi_isl_450703_Illinois_20200415_null_19":"background",
"epi_isl_450721_Wisconsin_20200401_null_28229":"background",
"epi_isl_450723_Bangkok_20200320_null_388":"background"
}
},
"timers":{
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"timer":1
},
"Primary SLAC analysis":{
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},
"Total time":{
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}
}
}