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Accession: PRJNA779404 ID: 779404

Florfenicol treatment and the piglet gut microbiome

For this longitudinal study, the influence of sow colostrum/ milk and florfenicol administration to piglets on the development of the pig gut microbiome was investigated using 16S rRNA gene and shotgun metagenomic sequencing.
AccessionPRJNA779404
Data TypeGenome sequencing and assembly
ScopeMultispecies
Publications
  • Published online: Holman D et al., "Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes", mSystems, 2024;
SubmissionRegistration date: 10-Nov-2021
Agriculture and Agri-Food Canada
RelevanceAgricultural
Project Data:
Resource NameNumber
of Links
Sequence data
Nucleotide (WGS master)1547
SRA Experiments1137
Other datasets
BioSample2303
Assembly1547
Assembly details:
Assembly levelNumber of Assemblies
1546
1546
AssemblyLevelWGSBioSampleInfraspecies IdTaxonomy
GCA_034115225.1ContigJAXEUF000000000SAMN37949123
SUG2301
GCA_034090965.1ContigJAXDRQ000000000SAMN37948371
SUG2300
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SUG2635
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SUG3075
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SUG3077
GCA_034088025.1ContigJAXDXE000000000SAMN37948528
SUG3078
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SUG3637
GCA_034118945.1ContigJAXFAI000000000SAMN37949288
SUG3638
GCA_034183235.1ContigJAXFLL000000000SAMN37949574
SUG3644
GCA_034177305.1ContigJAXFSV000000000SAMN37949767
SUG3645
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SUG3643
GCA_034099485.1ContigJAXENE000000000SAMN37948939
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SUG2203
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SUG2335
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SUG2648
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SUG3101
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SUG3162
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SUG3143
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SUG3147
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SUG3142
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SUG3047
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SUG2654
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SUG3090
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SUG3087
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SUG3086
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SUG3089
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SUG3088
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SUG3085
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SUG3017
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SUG3007
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SUG3019
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SUG3022
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SUG3015
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SUG3018
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SUG3021
GCA_034176155.1ContigJAXFUQ000000000SAMN37949814
SUG2996
GCA_034175705.1ContigJAXFVL000000000SAMN37949833
SUG3020
GCA_034177525.1ContigJAXFSQ000000000SAMN37949759
SUG3016
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SUG2997
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SUG2206
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SUG2207
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SUG2209
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SUG2248
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SUG2246
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SUG2250
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SUG2238
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SUG2237
GCA_034087945.1ContigJAXDXK000000000SAMN37948534
SUG2454
GCA_034087405.1ContigJAXDYM000000000SAMN37948533
SUG2407
GCA_034086365.1ContigJAXEAR000000000SAMN37948611
SUG2453
GCA_034179485.1ContigJAXFPV000000000SAMN37949684
SUG2490
GCA_034179705.1ContigJAXFPP000000000SAMN37949682
SUG2408
GCA_034179605.1ContigJAXFPW000000000SAMN37949680
SUG2400
GCA_034179745.1ContigJAXFPO000000000SAMN37949681
SUG2406
GCA_034179155.1ContigJAXFQD000000000SAMN37949683
SUG2448
GCA_034180895.1ContigJAXFNL000000000SAMN37949627
SUG2456
GCA_034180625.1ContigJAXFNZ000000000SAMN37949624
SUG2395
GCA_034180125.1ContigJAXFOV000000000SAMN37949626
SUG2447
GCA_034180405.1ContigJAXFOJ000000000SAMN37949631
SUG2493
GCA_034169825.1ContigJAXFII000000000SAMN37949487
SUG2398
GCA_034171395.1ContigJAXFGF000000000SAMN37949437
SUG2445
GCA_034174525.1ContigJAXFBY000000000SAMN37949318
SUG2492
GCA_034174645.1ContigJAXFWQ000000000SAMN37949860
SUG2452
GCA_034175835.1ContigJAXFVJ000000000SAMN37949822
SUG2451
GCA_034176765.1ContigJAXFTN000000000SAMN37949779
SUG2458
GCA_034177185.1ContigJAXFSY000000000SAMN37949771
SUG2404
GCA_034177935.1ContigJAXFSK000000000SAMN37949755
SUG2450
GCA_034178415.1ContigJAXFRM000000000SAMN37949729
SUG2449
GCA_034178285.1ContigJAXFRT000000000SAMN37949736
SUG2416
GCA_034113645.1ContigJAXEXA000000000SAMN37949179
SUG2418
GCA_034114305.1ContigJAXEVQ000000000SAMN37949162
SUG2417
GCA_034116505.1ContigJAXERM000000000SAMN37949056
SUG2489
GCA_034116705.1ContigJAXERC000000000SAMN37949046
SUG2401
GCA_034116305.1ContigJAXERW000000000SAMN37949054
SUG2443
GCA_034116545.1ContigJAXERK000000000SAMN37949057
SUG2491
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SUG2494
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SUG2444
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SUG2399
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SUG2455
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SUG2403
GCA_034102165.1ContigJAXEIH000000000SAMN37948813
SUG2415
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SUG2389
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SUG2442
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SUG2396
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SUG2405
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SUG2409
GCA_034101105.1ContigJAXEKJ000000000SAMN37948867
SUG2410
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SUG2402
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SUG3303
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SUG3305
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SUG3306
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SUG3322
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SUG3323
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SUG3318
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SUG3320
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SUG3304
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SUG3321
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SUG3310
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SUG3312
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SUG3325
GCA_034116105.1ContigJAXESE000000000SAMN37949066
SUG3307
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SUG3309
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SUG3308
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SUG3315
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SUG3316
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SUG3299
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SUG3324
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SUG3311
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SUG3300
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SUG3314
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SUG3301
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SUG3313
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SUG3319
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SUG3326
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SUG3427
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SUG3464
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SUG3463
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SUG3428
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SUG3522
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SUG3521
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SUG3166
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SUG3167
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SUG3169
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SUG3170
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SUG3172
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SUG3171
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SUG3168
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SUG3165
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SUG3173
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SUG3174
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SUG3176
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SUG3177
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SUG2656
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SUG2660
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SUG2662
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SUG3572
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SUG2669
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SUG2664
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SUG2670
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SUG2663
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SUG2673
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SUG2674
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SUG2675
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SUG2672
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SUG2666
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SUG2665
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SUG2668
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SUG2667
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SUG2671
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SUG2308
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SUG2306
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SUG2307
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SUG2305
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SUG3668
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SUG3671
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SUG3672
GCA_034103065.1ContigJAXEGN000000000SAMN37948795
SUG3667
GCA_034101185.1ContigJAXEKF000000000SAMN37948865
SUG3670
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SUG3669
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SUG3674
GCA_034178205.1ContigJAXFRY000000000SAMN37949750
SUG3673
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SUG2677
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SUG2676
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SUG2839
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SUG2840
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SUG2837
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SUG3100
GCA_034115065.1ContigJAXEUA000000000SAMN37949120
SUG3095
GCA_034109105.1ContigJAXEZF000000000SAMN37949258
SUG3098
GCA_034093655.1ContigJAXECG000000000SAMN37948658
SUG3097
GCA_034175165.1ContigJAXFVW000000000SAMN37949847
SUG3096
GCA_034168905.1ContigJAXFJJ000000000SAMN37949522
SUG2298
GCA_034088805.1ContigJAXDVP000000000SAMN37948488
SUG3346
GCA_034088665.1ContigJAXDVY000000000SAMN37948505
SUG3410
GCA_034089255.1ContigJAXDUR000000000SAMN37948468
SUG3348
GCA_034090355.1ContigJAXDST000000000SAMN37948415
SUG3347
GCA_034091925.1ContigJAXFWW000000000SAMN37949868
SUG3407
GCA_034091275.1ContigJAXFYK000000000SAMN37949913
SUG3408
GCA_034093595.1ContigJAXECH000000000SAMN37948661
SUG3353
GCA_034094275.1ContigJAXEBC000000000SAMN37948630
SUG3352
GCA_034104655.1ContigJAXEDI000000000SAMN37948689
SUG3354
GCA_034104385.1ContigJAXEDX000000000SAMN37948711
SUG3409
GCA_034103485.1ContigJAXEFT000000000SAMN37948748
SUG3356
GCA_034103905.1ContigJAXEEU000000000SAMN37948727
SUG3355
GCA_034101275.1ContigJAXEJZ000000000SAMN37948863
SUG3411
GCA_034101415.1ContigJAXEJS000000000SAMN37948847
SUG3357
GCA_034099875.1ContigJAXEMU000000000SAMN37948937
SUG3360
GCA_034099345.1ContigJAXENK000000000SAMN37948949
SUG3361
GCA_034099265.1ContigJAXENQ000000000SAMN37948955
SUG3362
GCA_034100055.1ContigJAXEMJ000000000SAMN37948920
SUG3358
GCA_034099955.1ContigJAXEMO000000000SAMN37948930
SUG3359
GCA_034114945.1ContigJAXEUL000000000SAMN37949131
SUG3370
GCA_034115125.1ContigJAXETX000000000SAMN37949121
SUG3369
GCA_034114405.1ContigJAXEVM000000000SAMN37949160
SUG3371
GCA_034115925.1ContigJAXESQ000000000SAMN37949087
SUG3366
GCA_034115505.1ContigJAXETK000000000SAMN37949108
SUG3368
GCA_034115745.1ContigJAXESY000000000SAMN37949097
SUG3367
GCA_034119165.1ContigJAXEZY000000000SAMN37949271
SUG3375
GCA_034118785.1ContigJAXFAO000000000SAMN37949292
SUG3376
GCA_034118185.1ContigJAXEOE000000000SAMN37948971
SUG3363
GCA_034118505.1ContigJAXFBF000000000SAMN37949311
SUG3377
GCA_034117185.1ContigJAXEQD000000000SAMN37949024
SUG3364
GCA_034116905.1ContigJAXEQT000000000SAMN37949038
SUG3365
GCA_034109025.1ContigJAXEZJ000000000SAMN37949260
SUG3374
GCA_034113785.1ContigJAXEWR000000000SAMN37949195
SUG3372
GCA_034113085.1ContigJAXEYB000000000SAMN37949223
SUG3373
GCA_034168705.1ContigJAXFJQ000000000SAMN37949529
SUG3391
GCA_034169135.1ContigJAXFIW000000000SAMN37949507
SUG3390
GCA_034168415.1ContigJAXFKA000000000SAMN37949539
SUG3393
GCA_034168525.1ContigJAXFJY000000000SAMN37949535
SUG3392
GCA_034168185.1ContigJAXFKF000000000SAMN37949545
SUG3394
GCA_034167145.1ContigJAXFLD000000000SAMN37949567
SUG3396
GCA_034167575.1ContigJAXFKS000000000SAMN37949562
SUG3395
GCA_034172565.1ContigJAXFET000000000SAMN37949406
SUG3383
GCA_034172755.1ContigJAXFEJ000000000SAMN37949390
SUG3382
GCA_034173065.1ContigJAXFDU000000000SAMN37949372
SUG3380
GCA_034173025.1ContigJAXFDW000000000SAMN37949386
SUG3381
GCA_034170845.1ContigJAXFHB000000000SAMN37949466
SUG3386
GCA_034171825.1ContigJAXFFU000000000SAMN37949432
SUG3384
GCA_034171355.1ContigJAXFGH000000000SAMN37949440
SUG3385
GCA_034169965.1ContigJAXFIE000000000SAMN37949495
SUG3389
GCA_034170485.1ContigJAXFHR000000000SAMN37949476
SUG3387
GCA_034170225.1ContigJAXFHY000000000SAMN37949484
SUG3388
GCA_034174985.1ContigJAXFWC000000000SAMN37949848
SUG3406
GCA_034174205.1ContigJAXFCO000000000SAMN37949345
SUG3379
GCA_034174565.1ContigJAXFBM000000000SAMN37949315
SUG3378
GCA_034176585.1ContigJAXFTX000000000SAMN37949795
SUG3405
GCA_034176845.1ContigJAXFTJ000000000SAMN37949783
SUG3404
GCA_034178165.1ContigJAXFSB000000000SAMN37949747
SUG3403
GCA_034178315.1ContigJAXFRS000000000SAMN37949739
SUG3402
GCA_034178585.1ContigJAXFRE000000000SAMN37949725
SUG3400
GCA_034178445.1ContigJAXFRL000000000SAMN37949733
SUG3401
GCA_034182055.1ContigJAXFML000000000SAMN37949603
SUG3397
GCA_034179825.1ContigJAXFPI000000000SAMN37949676
SUG3399
GCA_034181025.1ContigJAXFNK000000000SAMN37949662
SUG3398
GCA_034087245.1ContigJAXDYT000000000SAMN37948568
SUG3350
GCA_034087545.1ContigJAXDYE000000000SAMN37948560
SUG3349
GCA_034086445.1ContigJAXEAM000000000SAMN37948621
SUG3351
GCA_034178855.1ContigJAXFQP000000000SAMN37949715
SUG3666
GCA_034172355.1ContigJAXFFC000000000SAMN37949412
SUG3678
GCA_034114085.1ContigJAXEWB000000000SAMN37949176
SUG3679
GCA_034116945.1ContigJAXEQQ000000000SAMN37949040
SUG3675
GCA_034100265.1ContigJAXELY000000000SAMN37948921
SUG3665
GCA_034120015.1ContigJAXEIF000000000SAMN37948857
SUG3664
GCA_034103225.1ContigJAXEGF000000000SAMN37948772
SUG2495
GCA_034093615.1ContigJAXECJ000000000SAMN37948662
SUG2496
GCA_034099565.1ContigJAXEMZ000000000SAMN37948934
SUG2497
GCA_034119015.1ContigJAXFAE000000000SAMN37949281
SUG2498
GCA_034167185.1ContigJAXFLC000000000SAMN37949565
SUG2373
GCA_034103105.1ContigJAXEGK000000000SAMN37948767
SUG2375
GCA_034090475.1ContigJAXDSM000000000SAMN37948376
SUG2374
GCA_034113605.1ContigJAXEXC000000000SAMN37949201
SUG2376
GCA_034113445.1ContigJAXEXI000000000SAMN37949209
SUG2378
GCA_034090765.1ContigJAXDRY000000000SAMN37948377
SUG2377
GCA_034178945.1ContigJAXFQL000000000SAMN37949704
SUG2379
GCA_034088065.1ContigJAXDXD000000000SAMN37948526
SUG2380
GCA_034102725.1ContigJAXEHE000000000SAMN37948768
SUG2381
GCA_034173715.1ContigJAXFDF000000000SAMN37949361
SUG2382
GCA_034091045.1ContigJAXDRL000000000SAMN37948378
SUG2384
GCA_034100745.1ContigJAXELB000000000SAMN37948888
SUG2385
GCA_034168925.1ContigJAXFJH000000000SAMN37949519
SUG2383
GCA_034118745.1ContigJAXFAS000000000SAMN37949295
SUG2386
GCA_034116005.1ContigJAXESK000000000SAMN37949079
SUG2387
GCA_034180605.1ContigJAXFOA000000000SAMN37949654
SUG3084
GCA_034089165.1ContigJAXDUW000000000SAMN37948463
SUG3083
GCA_034178865.1ContigJAXFQQ000000000SAMN37949714
SUG3653
GCA_034174925.1ContigJAXFWD000000000SAMN37949852
SUG3660
GCA_034176075.1ContigJAXFUU000000000SAMN37949818
SUG3658
GCA_034178245.1ContigJAXFRX000000000SAMN37949749
SUG3657
GCA_034169415.1ContigJAXFIR000000000SAMN37949506
SUG3656
GCA_034089355.1ContigJAXDVE000000000SAMN37948479
SUG3661
GCA_034091625.1ContigJAXFXO000000000SAMN37949889
SUG3659
GCA_034118665.1ContigJAXFAV000000000SAMN37949303
SUG3652
GCA_034117865.1ContigJAXEOV000000000SAMN37948992
SUG3654
GCA_034167165.1ContigJAXEWY000000000SAMN37949200
SUG3655
GCA_034092005.1ContigJAXFWU000000000SAMN37949872
SUG3662
GCA_034176295.1ContigJAXFUK000000000SAMN37949807
SUG3651
GCA_034091795.1ContigJAXFXH000000000SAMN37949878
SUG2765
GCA_034167915.1ContigJAXFKL000000000SAMN37949550
SUG3613
GCA_034091065.1ContigJAXDRI000000000SAMN37948410
SUG3614
GCA_034104065.1ContigJAXEEN000000000SAMN37948719
SUG3612
GCA_034168245.1ContigJAXFKE000000000SAMN37949541
SUG3615
GCA_034090525.1ContigJAXDSK000000000SAMN37948411
SUG3731
GCA_034093575.1ContigJAXECK000000000SAMN37948665
SUG3039
GCA_034103885.1ContigJAXEEW000000000SAMN37948725
SUG3040
GCA_034115205.1ContigJAXEUK000000000SAMN37949130
SUG3041
GCA_034181725.1ContigJAXFMS000000000SAMN37949609
SUG3042
GCA_034115345.1ContigJAXETS000000000SAMN37949112
SUG2299
GCA_034102025.1ContigJAXEIN000000000SAMN37948850
SUG3457
GCA_034113405.1ContigJAXEXM000000000SAMN37949211
SUG2244
GCA_034168865.1ContigJAXFJI000000000SAMN37949518
SUG2245
GCA_034099245.1ContigJAXENN000000000SAMN37948957
SUG3682
GCA_034104405.1ContigJAXEDW000000000SAMN37948714
SUG3683
GCA_034113105.1ContigJAXEYA000000000SAMN37949229
SUG3684
GCA_034119145.1ContigJAXEZX000000000SAMN37949274
SUG3685
GCA_034118365.1ContigJAXFBQ000000000SAMN37949329
SUG3687
GCA_034118525.1ContigJAXFBE000000000SAMN37949314
SUG3686
GCA_034174225.1ContigJAXFCM000000000SAMN37949348
SUG3688
GCA_034171605.1ContigJAXFGA000000000SAMN37949434
SUG3689
GCA_034174405.1ContigJAXFCB000000000SAMN37949330
SUG3702
GCA_034176025.1ContigJAXFUZ000000000SAMN37949831
SUG3694
GCA_034176635.1ContigJAXFTU000000000SAMN37949798
SUG3710
GCA_034176475.1ContigJAXFUB000000000SAMN37949797
SUG3696
GCA_034175995.1ContigJAXFUY000000000SAMN37949832
SUG3697
GCA_034176825.1ContigJAXFTK000000000SAMN37949785
SUG3693
GCA_034176905.1ContigJAXFTG000000000SAMN37949786
SUG3700
GCA_034178185.1ContigJAXFSA000000000SAMN37949751
SUG3716
GCA_034178265.1ContigJAXFRW000000000SAMN37949741
SUG3707
GCA_034177655.1ContigJAXFSJ000000000SAMN37949763
SUG3711
GCA_034182605.1ContigJAXFLZ000000000SAMN37949593
SUG3715
GCA_034117965.1ContigJAXEOQ000000000SAMN37948993
SUG3690
GCA_034117105.1ContigJAXEQF000000000SAMN37949028
SUG3717
GCA_034114785.1ContigJAXEUU000000000SAMN37949147
SUG3724
GCA_034115685.1ContigJAXETB000000000SAMN37949101
SUG3704
GCA_034116385.1ContigJAXERS000000000SAMN37949073
SUG3713
GCA_034119205.1ContigJAXEZT000000000SAMN37949275
SUG3709
GCA_034113305.1ContigJAXEXQ000000000SAMN37949230
SUG3714
GCA_034104145.1ContigJAXEEK000000000SAMN37948716
SUG3698
GCA_034104325.1ContigJAXEEA000000000SAMN37948717
SUG3705
GCA_034104305.1ContigJAXEEB000000000SAMN37948715
SUG3691
GCA_034104855.1ContigJAXEDA000000000SAMN37948684
SUG3712
GCA_034101755.1ContigJAXEJC000000000SAMN37948858
SUG3692
GCA_034100255.1ContigJAXEMA000000000SAMN37948922
SUG3695
GCA_034100245.1ContigJAXELW000000000SAMN37948909
SUG3699
GCA_034100325.1ContigJAXELX000000000SAMN37948910
SUG3723
GCA_034091905.1ContigJAXFWY000000000SAMN37949873
SUG3706
GCA_034089825.1ContigJAXDTU000000000SAMN37948480
SUG3701
GCA_034088965.1ContigJAXDVJ000000000SAMN37948481
SUG3708
GCA_034088785.1ContigJAXDVS000000000SAMN37948490
SUG3681
GCA_034088545.1ContigJAXDWE000000000SAMN37948509
SUG3703
GCA_034119265.1ContigJAXEZR000000000SAMN37949276
SUG3719
GCA_034086805.1ContigJAXDZQ000000000SAMN37948600
SUG3718
GCA_034179735.1ContigJAXFPR000000000SAMN37949699
SUG3680
GCA_034170905.1ContigJAXFGY000000000SAMN37949456
SUG2220
GCA_034116225.1ContigJAXESB000000000SAMN37949053
SUG2334
GCA_034099125.1ContigJAXENT000000000SAMN37948958
SUG2388
GCA_034090045.1ContigJAXDTI000000000SAMN37948423
SUG2221
GCA_034102625.1ContigJAXEHJ000000000SAMN37948787
SUG3137
GCA_034115385.1ContigJAXETP000000000SAMN37949110
SUG3130
GCA_034169005.1ContigJAXFJC000000000SAMN37949515
SUG3133
GCA_034171285.1ContigJAXFGI000000000SAMN37949441
SUG3132
GCA_034172205.1ContigJAXFFL000000000SAMN37949418
SUG3131
GCA_034176435.1ContigJAXFUD000000000SAMN37949801
SUG3135
GCA_034175545.1ContigJAXFVM000000000SAMN37949834
SUG3136
GCA_034183435.1ContigJAXFLH000000000SAMN37949571
SUG3134
GCA_034102585.1ContigJAXEHK000000000SAMN37948786
SUG3129
GCA_034090435.1ContigJAXDSO000000000SAMN37948393
SUG2938
GCA_034169645.1ContigJAXFIL000000000SAMN37949490
SUG2939
GCA_034174935.1ContigJAXFWE000000000SAMN37949853
SUG3735
GCA_034100025.1ContigJAXEMK000000000SAMN37948926
SUG2788
GCA_034093515.1ContigJAXECL000000000SAMN37948664
SUG2633
GCA_034113525.1ContigJAXEXF000000000SAMN37949204
SUG3646
GCA_034091825.1ContigJAXFXD000000000SAMN37949883
SUG3648
GCA_034176195.1ContigJAXFUO000000000SAMN37949811
SUG3647
GCA_034091025.1ContigJAXDRK000000000SAMN37948372
SUG2310
GCA_034116645.1ContigJAXERE000000000SAMN37949047
SUG2696
GCA_034099645.1ContigJAXEMT000000000SAMN37948932
SUG2699
GCA_034114245.1ContigJAXEVU000000000SAMN37949168
SUG3640
GCA_034112845.1ContigJAXEYP000000000SAMN37949241
SUG3641
GCA_034088225.1ContigJAXDWT000000000SAMN37948516
SUG3639
GCA_034105765.1ContigJAXECR000000000SAMN37948670
SUG3642
GCA_034102445.1ContigJAXEHT000000000SAMN37948801
SUG2741
SRA Data Details
ParameterValue
Data volume, Gbases5,220
Data volume, Tbytes1.69

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