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comparison test-data/summary/nsp8.FEL.json @ 3:c046f72e5e3a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 06:58:21 +0000
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2:fb833dd994f2 3:c046f72e5e3a
1 {
2 "MLE":{
3 "content":{
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204 },
205 "headers": [
206 ["alpha", "Synonymous substitution rate at a site"],
207 ["beta", "Non-synonymous substitution rate at a site"],
208 ["alpha=beta", "The rate estimate under the neutral model"],
209 ["LRT", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"],
210 ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
211 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
212 ]
213 },
214 "analysis":{
215 "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
216 "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",
217 "contact":"spond@temple.edu",
218 "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\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, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
219 "requirements":"in-frame codon alignment and a phylogenetic tree",
220 "version":"2.1"
221 },
222 "branch attributes":{
223 "0":{
224 "Node20":{
225 "Global MG94xREV":0.001634412620939209,
226 "Nucleotide GTR":0.001684521619549293
227 },
228 "Node38":{
229 "Global MG94xREV":0.001735516186079463,
230 "Nucleotide GTR":0.00168484920326581
231 },
232 "Node4":{
233 "Global MG94xREV":0.001634082124264937,
234 "Nucleotide GTR":0.001683801387489096
235 },
236 "REFERENCE":{
237 "Global MG94xREV":0,
238 "Nucleotide GTR":0,
239 "original name":"REFERENCE"
240 },
241 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
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245 },
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249 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
250 },
251 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
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255 },
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260 },
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263 "Nucleotide GTR":0.001684401404203384,
264 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
265 },
266 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
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269 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
270 },
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275 },
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300 },
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341 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
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351 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
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354 "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human"
355 },
356 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":{
357 "Global MG94xREV":0.003464011570187254,
358 "Nucleotide GTR":0.003373764235314068,
359 "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human"
360 },
361 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{
362 "Global MG94xREV":0.005236219940276191,
363 "Nucleotide GTR":0.005068409188375663,
364 "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human"
365 },
366 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
367 "Global MG94xREV":0.003464842731605314,
368 "Nucleotide GTR":0.003372774424770855,
369 "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human"
370 },
371 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
372 "Global MG94xREV":0.001735902734225727,
373 "Nucleotide GTR":0.001686266012390882,
374 "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human"
375 },
376 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
377 "Global MG94xREV":0.003480097455920979,
378 "Nucleotide GTR":0.003374436490976879,
379 "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human"
380 },
381 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
382 "Global MG94xREV":0.003472571057360136,
383 "Nucleotide GTR":0.003376034743011948,
384 "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human"
385 },
386 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
387 "Global MG94xREV":0.003474988473611597,
388 "Nucleotide GTR":0.003374190741831846,
389 "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human"
390 },
391 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
392 "Global MG94xREV":0.003471294890480852,
393 "Nucleotide GTR":0.003376937492543959,
394 "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human"
395 }
396 },
397 "attributes":{
398 "Global MG94xREV":{
399 "attribute type":"branch length",
400 "display order":1
401 },
402 "Nucleotide GTR":{
403 "attribute type":"branch length",
404 "display order":0
405 },
406 "original name":{
407 "attribute type":"node label",
408 "display order":-1
409 }
410 }
411 },
412 "data partitions":{
413 "0":{
414 "coverage": [
415 [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, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
416 ],
417 "name":"fel.filter.default"
418 }
419 },
420 "fits":{
421 "Global MG94xREV":{
422 "AIC-c":2512.96200112621,
423 "Equilibrium frequencies": [
424 [0.03825952761243274],
425 [0.01370948533169502],
426 [0.0238326285579188],
427 [0.05169206288834598],
428 [0.02910782227384961],
429 [0.01043016700423795],
430 [0.01813184740308045],
431 [0.03932728586627101],
432 [0.01035067712195123],
433 [0.003708944282165923],
434 [0.006447644771501305],
435 [0.01398469573761802],
436 [0.0283653688047424],
437 [0.01016412464618009],
438 [0.01766935821790241],
439 [0.03832416445281453],
440 [0.01521889661505549],
441 [0.005453366858635389],
442 [0.009480156518454269],
443 [0.02056209812326697],
444 [0.01157852606970437],
445 [0.004148917752546374],
446 [0.007212496554133422],
447 [0.01564363009947405],
448 [0.00411729822204095],
449 [0.001475345962268018],
450 [0.002564747797779777],
451 [0.005562840210150803],
452 [0.01128319250724396],
453 [0.004043091272315801],
454 [0.007028527343480687],
455 [0.01524460789411934],
456 [0.03592403244011121],
457 [0.01287261047188149],
458 [0.02237780168434643],
459 [0.04853659885475865],
460 [0.02733097915424774],
461 [0.009793473186905268],
462 [0.01702501611901085],
463 [0.03692661100139533],
464 [0.009718835644621534],
465 [0.003482537371104292],
466 [0.0060540580187001],
467 [0.01313102107355921],
468 [0.02663384763763138],
469 [0.009543670983435077],
470 [0.01659075888876379],
471 [0.0359847236220365],
472 [0.00848480075962617],
473 [0.03199221880690793],
474 [0.01801483181642438],
475 [0.006455230577911434],
476 [0.01122180073845716],
477 [0.02433965804833868],
478 [0.002295465694104339],
479 [0.003990447484454917],
480 [0.008655128485630147],
481 [0.01755532734880559],
482 [0.00629057695692368],
483 [0.01093556617204019],
484 [0.02371882618448924]
485 ],
486 "Log Likelihood":-1205.05897637469,
487 "Rate Distributions":{
488 "non-synonymous/synonymous rate ratio for *background*": [
489 [0.4929148115423557, 1]
490 ],
491 "non-synonymous/synonymous rate ratio for *test*": [
492 [24.31954781803373, 1]
493 ]
494 },
495 "display order":1,
496 "estimated parameters":51
497 },
498 "Nucleotide GTR":{
499 "AIC-c":2633.0046471406,
500 "Equilibrium frequencies": [
501 [0.3251262626262627],
502 [0.1799242424242424],
503 [0.2026515151515151],
504 [0.2922979797979798]
505 ],
506 "Log Likelihood":-1247.247280799152,
507 "Rate Distributions":{
508 "Substitution rate from nucleotide A to nucleotide C":0,
509 "Substitution rate from nucleotide A to nucleotide G":1,
510 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
511 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
512 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
513 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
514 },
515 "display order":0,
516 "estimated parameters":69
517 }
518 },
519 "input":{
520 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
521 "number of sequences":32,
522 "number of sites":198,
523 "partition count":1,
524 "trees":{
525 "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
526 }
527 },
528 "tested":{
529 "0":{
530 "Node20":"test",
531 "Node38":"background",
532 "Node4":"test",
533 "REFERENCE":"background",
534 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
535 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
536 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
537 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
538 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
539 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
540 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
541 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
542 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
543 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
544 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
545 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
546 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
547 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
548 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
549 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
550 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
551 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
552 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
553 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",
554 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
555 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",
556 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",
557 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",
558 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
559 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",
560 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",
561 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",
562 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",
563 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",
564 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"
565 }
566 },
567 "timers":{
568 "FEL analysis":{
569 "order":2,
570 "timer":4
571 },
572 "Model fitting":{
573 "order":1,
574 "timer":6
575 },
576 "Total time":{
577 "order":0,
578 "timer":10
579 }
580 }
581 }