comparison test-data/summary/nsp8.PRIME.json @ 26:60eec78ee26f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:00:42 +0000
parents
children
comparison
equal deleted inserted replaced
25:5e8d0e777033 26:60eec78ee26f
1 {
2 "MLE":{
3 "content":{
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201 [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
202 [0, 1.231388513343972, 0.000158458220515845, -13.77233562678079, -13.77239892102621, 1, 0.03644798756061563, 1, -13.77190817477141, -0.3104805457700024, 1, -13.77191376864584, 0.2357212180710769, 1, -13.77190817477141, -0.03138277695602196, 1, -13.77191376864584, -0.005528760550374304, 1, -13.7719081747714]
203 ]
204 },
205 "headers": [
206 ["alpha;", "Synonymous substitution rate at a site"],
207 ["β", "Log of property independent non-synonymous rate a site"],
208 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
209 ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
210 ["FEL LogL", "Site Log-likelihood under the FEL model"],
211 ["p-value", "Omnibus p-value (any property is important)"],
212 ["λ1", "Importance for Factor I bipolar"],
213 ["p1", "p-value for non-zero effect of Factor I bipolar"],
214 ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"],
215 ["λ2", "Importance for Factor II secondary structure"],
216 ["p2", "p-value for non-zero effect of Factor II secondary structure"],
217 ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"],
218 ["λ3", "Importance for Factor III volume"],
219 ["p3", "p-value for non-zero effect of Factor III volume"],
220 ["LogL3", "Log likelihood when there is no effect of Factor III volume"],
221 ["λ4", "Importance for Factor IV composition"],
222 ["p4", "p-value for non-zero effect of Factor IV composition"],
223 ["LogL4", "Log likelihood when there is no effect of Factor IV composition"],
224 ["λ5", "Importance for Factor V charge"],
225 ["p5", "p-value for non-zero effect of Factor V charge"],
226 ["LogL5", "Log likelihood when there is no effect of Factor V charge"]
227 ]
228 },
229 "analysis":{
230 "authors":"Sergei L. Kosakovsky Pond",
231 "citation":"TBD",
232 "contact":"spond@temple.edu",
233 "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n 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 ",
234 "requirements":"in-frame codon alignment and a phylogenetic tree",
235 "version":"0.0.1"
236 },
237 "branch attributes":{
238 "0":{
239 "Node20":{
240 "Global MG94xREV":0.001634412628363601,
241 "Nucleotide GTR":0.001684521619549293
242 },
243 "Node38":{
244 "Global MG94xREV":0.001735516181127408,
245 "Nucleotide GTR":0.00168484920326581
246 },
247 "Node4":{
248 "Global MG94xREV":0.001634082125054255,
249 "Nucleotide GTR":0.001683801387489096
250 },
251 "REFERENCE":{
252 "Global MG94xREV":0,
253 "Nucleotide GTR":0,
254 "original name":"REFERENCE"
255 },
256 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
257 "Global MG94xREV":0,
258 "Nucleotide GTR":0,
259 "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
260 },
261 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
262 "Global MG94xREV":0.001732287226413535,
263 "Nucleotide GTR":0.001682745450340891,
264 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
265 },
266 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
267 "Global MG94xREV":0,
268 "Nucleotide GTR":0,
269 "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
270 },
271 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
272 "Global MG94xREV":0.001731614558297581,
273 "Nucleotide GTR":0.00168274558227101,
274 "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
275 },
276 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
277 "Global MG94xREV":0.001735723689760284,
278 "Nucleotide GTR":0.001684401404203384,
279 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
280 },
281 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
282 "Global MG94xREV":0.001732400224923104,
283 "Nucleotide GTR":0.00168406792173386,
284 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
285 },
286 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
287 "Global MG94xREV":0.001734572372218793,
288 "Nucleotide GTR":0.001684975469042935,
289 "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
290 },
291 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
292 "Global MG94xREV":0.001735567212797747,
293 "Nucleotide GTR":0.001684401583391051,
294 "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
295 },
296 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
297 "Global MG94xREV":0.001732287290600434,
298 "Nucleotide GTR":0.001682745512695379,
299 "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
300 },
301 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
302 "Global MG94xREV":0,
303 "Nucleotide GTR":0,
304 "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
305 },
306 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
307 "Global MG94xREV":0.001733756929863212,
308 "Nucleotide GTR":0.001684431017860219,
309 "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
310 },
311 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
312 "Global MG94xREV":0.001733765372843661,
313 "Nucleotide GTR":0.001684439221071522,
314 "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
315 },
316 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
317 "Global MG94xREV":0,
318 "Nucleotide GTR":0,
319 "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
320 },
321 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
322 "Global MG94xREV":0.001736016199323374,
323 "Nucleotide GTR":0.00168443927661716,
324 "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
325 },
326 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
327 "Global MG94xREV":0.001733699172098583,
328 "Nucleotide GTR":0.001685171120971631,
329 "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
330 },
331 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
332 "Global MG94xREV":0.001733317353440973,
333 "Nucleotide GTR":0.001684401899924961,
334 "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
335 },
336 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
337 "Global MG94xREV":0.01050948249155059,
338 "Nucleotide GTR":0.01020457779555702,
339 "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
340 },
341 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
342 "Global MG94xREV":0.02683667579915389,
343 "Nucleotide GTR":0.02592331511084145,
344 "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
345 },
346 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
347 "Global MG94xREV":0.005257318382497578,
348 "Nucleotide GTR":0.005093980037543817,
349 "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human"
350 },
351 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
352 "Global MG94xREV":0.003479916215882181,
353 "Nucleotide GTR":0.003379296026417724,
354 "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human"
355 },
356 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
357 "Global MG94xREV":0.003464849064677958,
358 "Nucleotide GTR":0.003372774424630234,
359 "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
360 },
361 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
362 "Global MG94xREV":0.00347332934630856,
363 "Nucleotide GTR":0.003374190595560375,
364 "original name":"gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human"
365 },
366 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
367 "Global MG94xREV":0.00521423750425419,
368 "Nucleotide GTR":0.00505933790460295,
369 "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"
370 },
371 "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":{
372 "Global MG94xREV":0.003464011560303172,
373 "Nucleotide GTR":0.003373764235314068,
374 "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"
375 },
376 "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":{
377 "Global MG94xREV":0.005236219925335357,
378 "Nucleotide GTR":0.005068409188375663,
379 "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"
380 },
381 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
382 "Global MG94xREV":0.003464842721718857,
383 "Nucleotide GTR":0.003372774424770855,
384 "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"
385 },
386 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
387 "Global MG94xREV":0.001735902729272567,
388 "Nucleotide GTR":0.001686266012390882,
389 "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"
390 },
391 "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":{
392 "Global MG94xREV":0.003480097445990996,
393 "Nucleotide GTR":0.003374436490976879,
394 "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"
395 },
396 "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":{
397 "Global MG94xREV":0.003472571047451632,
398 "Nucleotide GTR":0.003376034743011948,
399 "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"
400 },
401 "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":{
402 "Global MG94xREV":0.003474988463696198,
403 "Nucleotide GTR":0.003374190741831846,
404 "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"
405 },
406 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
407 "Global MG94xREV":0.003471294880575992,
408 "Nucleotide GTR":0.003376937492543959,
409 "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"
410 }
411 },
412 "attributes":{
413 "Global MG94xREV":{
414 "attribute type":"branch length",
415 "display order":1
416 },
417 "Nucleotide GTR":{
418 "attribute type":"branch length",
419 "display order":0
420 },
421 "original name":{
422 "attribute type":"node label",
423 "display order":-1
424 }
425 }
426 },
427 "data partitions":{
428 "0":{
429 "coverage": [
430 [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]
431 ],
432 "name":"prime.filter.default"
433 }
434 },
435 "fits":{
436 "Global MG94xREV":{
437 "AIC-c":2512.962001128159,
438 "Equilibrium frequencies": [
439 [0.03825952761243274],
440 [0.01370948533169502],
441 [0.0238326285579188],
442 [0.05169206288834598],
443 [0.02910782227384961],
444 [0.01043016700423795],
445 [0.01813184740308045],
446 [0.03932728586627101],
447 [0.01035067712195123],
448 [0.003708944282165923],
449 [0.006447644771501305],
450 [0.01398469573761802],
451 [0.0283653688047424],
452 [0.01016412464618009],
453 [0.01766935821790241],
454 [0.03832416445281453],
455 [0.01521889661505549],
456 [0.005453366858635389],
457 [0.009480156518454269],
458 [0.02056209812326697],
459 [0.01157852606970437],
460 [0.004148917752546374],
461 [0.007212496554133422],
462 [0.01564363009947405],
463 [0.00411729822204095],
464 [0.001475345962268018],
465 [0.002564747797779777],
466 [0.005562840210150803],
467 [0.01128319250724396],
468 [0.004043091272315801],
469 [0.007028527343480687],
470 [0.01524460789411934],
471 [0.03592403244011121],
472 [0.01287261047188149],
473 [0.02237780168434643],
474 [0.04853659885475865],
475 [0.02733097915424774],
476 [0.009793473186905268],
477 [0.01702501611901085],
478 [0.03692661100139533],
479 [0.009718835644621534],
480 [0.003482537371104292],
481 [0.0060540580187001],
482 [0.01313102107355921],
483 [0.02663384763763138],
484 [0.009543670983435077],
485 [0.01659075888876379],
486 [0.0359847236220365],
487 [0.00848480075962617],
488 [0.03199221880690793],
489 [0.01801483181642438],
490 [0.006455230577911434],
491 [0.01122180073845716],
492 [0.02433965804833868],
493 [0.002295465694104339],
494 [0.003990447484454917],
495 [0.008655128485630147],
496 [0.01755532734880559],
497 [0.00629057695692368],
498 [0.01093556617204019],
499 [0.02371882618448924]
500 ],
501 "Log Likelihood":-1205.058976375664,
502 "Rate Distributions":{
503 "non-synonymous/synonymous rate ratio for *background*": [
504 [0.4929148115989916, 1]
505 ],
506 "non-synonymous/synonymous rate ratio for *test*": [
507 [24.3195468932995, 1]
508 ]
509 },
510 "display order":1,
511 "estimated parameters":51
512 },
513 "Nucleotide GTR":{
514 "AIC-c":2633.0046471406,
515 "Equilibrium frequencies": [
516 [0.3251262626262627],
517 [0.1799242424242424],
518 [0.2026515151515151],
519 [0.2922979797979798]
520 ],
521 "Log Likelihood":-1247.247280799152,
522 "Rate Distributions":{
523 "Substitution rate from nucleotide A to nucleotide C":0,
524 "Substitution rate from nucleotide A to nucleotide G":1,
525 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
526 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
527 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
528 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
529 },
530 "display order":0,
531 "estimated parameters":69
532 }
533 },
534 "input":{
535 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
536 "number of sequences":32,
537 "number of sites":198,
538 "partition count":1,
539 "trees":{
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541 }
542 },
543 "tested":{
544 "0":{
545 "Node20":"test",
546 "Node38":"background",
547 "Node4":"test",
548 "REFERENCE":"background",
549 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
550 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
551 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
552 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
553 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
554 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
555 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
556 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
557 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
558 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
559 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
560 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
561 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
562 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
563 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
564 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
565 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
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567 "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",
568 "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",
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570 "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",
571 "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",
572 "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",
573 "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",
574 "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",
575 "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",
576 "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",
577 "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",
578 "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",
579 "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"
580 }
581 },
582 "timers":{
583 "Model fitting":{
584 "order":1,
585 "timer":5
586 },
587 "PRIME analysis":{
588 "order":2,
589 "timer":19
590 },
591 "Total time":{
592 "order":0,
593 "timer":25
594 }
595 }
596 }