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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads sample | ||
| Bacteria 2 D 253384 2019 255403 0.96905 SS2 | ||
| Archaea 2157 D 3449 42 3491 0.01325 SS2 | ||
| Eukaryota 2759 D 365 89 454 0.00172 SS2 | ||
| Viruses 10239 D 4211 0 4211 0.01598 SS2 | ||
| Bacteria 2 D 234049 244 234293 0.97618 2A | ||
| Archaea 2157 D 3292 6 3298 0.01374 2A | ||
| Eukaryota 2759 D 133 3 136 5.7e-4 2A | ||
| Viruses 10239 D 2282 0 2282 0.00951 2A | ||
| Bacteria 2 D 202759 205 202964 0.97524 6C | ||
| Archaea 2157 D 2545 4 2549 0.01225 6C | ||
| Eukaryota 2759 D 89 2 91 4.4e-4 6C | ||
| Viruses 10239 D 2513 0 2513 0.012070000000000001 6C | ||
| Bacteria 2 D 193163 177 193340 0.97477 2C | ||
| Archaea 2157 D 2649 4 2653 0.01338 2C | ||
| Eukaryota 2759 D 614 15 629 0.00317 2C | ||
| Viruses 10239 D 1722 0 1722 0.00868 2C | ||
| Bacteria 2 D 360872 1804 362676 0.97937 SS1 | ||
| Archaea 2157 D 5467 47 5514 0.01489 SS1 | ||
| Eukaryota 2759 D 703 101 804 0.00217 SS1 | ||
| Viruses 10239 D 1319 0 1319 0.00356 SS1 | ||
| Bacteria 2 D 240929 211 241140 0.97468 6A | ||
| Archaea 2157 D 3466 5 3471 0.01403 6A | ||
| Eukaryota 2759 D 153 3 156 6.3e-4 6A | ||
| Viruses 10239 D 2638 0 2638 0.01066 6A | ||
| Bacteria 2 D 252899 268 253167 0.97557 1A | ||
| Archaea 2157 D 3622 6 3628 0.01398 1A | ||
| Eukaryota 2759 D 330 8 338 0.0013 1A | ||
| Viruses 10239 D 2374 0 2374 0.00915 1A | ||
| Bacteria 2 D 165343 164 165507 0.97526 1C | ||
| Archaea 2157 D 2328 3 2331 0.01374 1C | ||
| Eukaryota 2759 D 119 2 121 7.1e-4 1C | ||
| Viruses 10239 D 1744 0 1744 0.01028 1C |
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51,846
data/2023-12-22_bmc-cow-depletion/hv_hits_putative_all.tsv
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1,886 changes: 1,886 additions & 0 deletions
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data/2023-12-22_bmc-cow-depletion/hv_hits_putative_filtered.tsv
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data/2023-12-22_bmc-cow-depletion/qc_adapter_stats.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| sample percent_gc mean_seq_len n_read_pairs percent_duplicates n_bases_approx per_base_sequence_quality per_tile_sequence_quality per_sequence_quality_scores per_base_sequence_content per_sequence_gc_content per_base_n_content sequence_length_distribution sequence_duplication_levels overrepresented_sequences adapter_content stage | ||
| 1A 51 150 78451849 94.93462712046542 23400000000 pass/pass fail/fail warn/warn fail/fail pass/pass pass/pass pass/pass fail/fail warn/warn fail/fail raw_concat | ||
| 1C 51 150 47376584 94.16942468765848 14200000000 pass/pass fail/fail warn/pass fail/fail pass/pass pass/pass pass/pass fail/fail warn/warn fail/fail raw_concat | ||
| 2A 51 150 71130999 94.95240423949721 21200000000 pass/pass fail/fail warn/pass fail/fail pass/pass pass/pass pass/pass fail/fail warn/warn fail/fail raw_concat | ||
| 2C 51 150 49158246 93.42677984822313 14600000000 pass/pass fail/fail warn/warn fail/fail pass/pass pass/pass pass/pass fail/fail warn/warn fail/fail raw_concat | ||
| 6A 51 150 71192267 94.817930410275 21200000000 pass/pass fail/fail warn/pass fail/fail pass/pass pass/pass pass/pass fail/fail warn/warn fail/fail raw_concat | ||
| 6C 51 150 53655715 93.74559506275138 16000000000 pass/pass fail/fail warn/warn fail/fail pass/pass pass/pass pass/pass fail/fail warn/warn fail/fail raw_concat | ||
| SS1 51 150 61096105 91.61742981894301 18200000000 pass/pass fail/fail warn/warn fail/fail pass/pass pass/pass pass/pass fail/fail warn/warn fail/fail raw_concat | ||
| SS2 50 150 39146173 90.72005001240018 11600000000 warn/pass fail/fail warn/warn fail/fail warn/pass pass/pass pass/pass fail/fail fail/warn fail/fail raw_concat | ||
| 1A 51 133.8680771459585 65476301 96.2554841175091 17400000000 pass/pass fail/fail warn/pass fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass cleaned | ||
| 1C 51 132.7943818065906 40169799 95.3012205067167 10600000000 pass/pass fail/fail warn/pass fail/fail pass/pass pass/pass warn/warn fail/fail warn/warn pass/pass cleaned | ||
| 2A 51 133.8210224632644 59990791 95.96230957773497 16000000000 pass/pass fail/fail warn/pass fail/fail pass/pass pass/pass warn/warn fail/fail warn/warn pass/pass cleaned | ||
| 2C 51 135.9326951584075 40816343 95.22968500547375 11000000000 pass/pass fail/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass cleaned | ||
| 6A 51 135.0995848516524 59731901 95.9628713760691 16000000000 pass/pass fail/fail warn/pass fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass cleaned | ||
| 6C 51 133.0791847046676 44075930 95.46884644870812 11600000000 pass/pass fail/fail warn/warn fail/fail pass/pass pass/pass warn/warn fail/fail warn/warn pass/pass cleaned | ||
| SS1 51 132.6186958110153 50058144 93.48542280139144 13200000000 pass/pass fail/fail warn/pass fail/fail pass/pass pass/pass warn/warn fail/fail warn/warn pass/pass cleaned | ||
| SS2 50 130.4142505343276 32226953 92.96294155910216 8300000000 pass/pass fail/fail warn/warn fail/fail fail/pass pass/pass warn/warn fail/fail fail/warn pass/pass cleaned | ||
| 1A 51 139.36255593487823 22854479 86.81675006592903 6200000000 pass/pass fail/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| 1C 51 139.20760796494162 14350237 85.61750284694082 3900000000 pass/pass fail/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| 2A 51 139.63913643462556 20423723 85.8468660681335 5600000000 pass/pass fail/fail warn/warn fail/fail pass/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| 2C 51 140.06709922712656 16005855 86.49501567215958 4400000000 pass/pass fail/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| 6A 51 140.12831535289862 22072047 89.67819507158768 6100000000 pass/pass fail/fail warn/pass fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| 6C 51 138.70188014663512 15982530 84.83473982320653 4300000000 pass/pass fail/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| SS1 51 138.4385150033175 19868839 75.97677361364332 5400000000 pass/pass fail/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| SS2 50 137.00414863944457 10599017 75.17372620686524 2800000000 warn/pass fail/fail warn/warn fail/fail fail/pass pass/pass warn/warn fail/fail warn/warn pass/pass dedup | ||
| 1A 51.5 136.75287636030419 3910063 73.98225906972313 1069100000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass ribo_initial | ||
| 1C 51.5 135.99041018098131 2414227 67.0889882457515 656400000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass ribo_initial | ||
| 2A 51.5 136.78196583592438 3488928 71.0065418147795 954100000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass ribo_initial | ||
| 2C 51 137.6302689054013 2783358 69.11198063419974 765800000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass ribo_initial | ||
| 6A 51.5 137.53608104443185 3724130 72.34358874639034 1024100000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass ribo_initial | ||
| 6C 51 135.7960863042931 3007081 68.69937809284741 816400000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail fail/warn pass/pass ribo_initial | ||
| SS1 51 136.4757104096983 4984131 63.52020254944111 1360100000 pass/pass fail/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass ribo_initial | ||
| SS2 50 136.18220473815117 3048362 58.21775872323245 830100000 pass/pass warn/fail warn/warn fail/fail warn/warn pass/pass warn/warn fail/fail warn/warn pass/pass ribo_initial | ||
| 1A 51.5 137.45718722448945 3875759 74.30301684944553 1065200000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_human | ||
| 1C 51.5 136.6982281575895 2395134 67.44908045917455 654700000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_human | ||
| 2A 51.5 137.43908098700615 3464173 71.23507445433462 952000000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_human | ||
| 2C 51 138.341321095727 2743238 69.96501895508351 758800000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_human | ||
| 6A 51.5 138.08580135512165 3700332 72.78083833287508 1021700000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_human | ||
| 6C 51 136.52978064202955 2982978 68.972459207336 814300000 pass/pass fail/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail fail/warn pass/pass remove_human | ||
| SS1 51 137.15302903584586 4929803 64.30977109270779 1352100000 pass/pass warn/fail warn/warn fail/warn pass/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_human | ||
| SS2 50 136.81779241580736 3023631 58.602481784790534 827200000 pass/pass warn/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_human | ||
| 1A 52 132.53457948102118 514626 52.396925734963446 136300000 pass/pass warn/fail warn/pass fail/warn warn/warn pass/pass warn/warn fail/fail warn/warn pass/pass ribo_secondary | ||
| 1C 51 132.06809382923592 359291 51.602619677314046 94800000 pass/pass fail/fail warn/pass fail/warn warn/warn pass/pass warn/warn fail/fail warn/warn pass/pass ribo_secondary | ||
| 2A 51 132.90090998849792 491215 53.66103925245045 130400000 pass/pass fail/fail warn/pass fail/warn warn/warn pass/pass warn/warn fail/fail warn/warn pass/pass ribo_secondary | ||
| 2C 51 134.6051500645506 400461 54.787950571275296 107700000 pass/pass fail/fail warn/pass fail/warn warn/warn pass/pass warn/warn fail/fail warn/warn pass/pass ribo_secondary | ||
| 6A 51.5 133.8721752635945 490621 52.327375211254264 131200000 pass/pass fail/fail warn/pass fail/warn warn/warn pass/pass warn/warn fail/fail warn/warn pass/pass ribo_secondary | ||
| 6C 51 131.97716621178287 435276 52.90787540491868 114800000 pass/pass fail/fail warn/warn fail/warn warn/warn pass/pass warn/warn fail/fail warn/warn pass/pass ribo_secondary | ||
| SS1 51 133.11592705319455 798390 45.71818773456421 212400000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn warn/warn warn/pass pass/pass ribo_secondary | ||
| SS2 50 135.031473260469 720151 40.02858728514213 194300000 pass/pass warn/fail warn/warn fail/fail warn/warn pass/pass warn/warn warn/warn warn/pass pass/pass ribo_secondary | ||
| 1A 51.5 137.5686135945349 3870217 74.33846052607655 1064500000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_other | ||
| 1C 51.5 136.8117368491253 2391647 67.51381597192815 654200000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_other | ||
| 2A 51.5 137.5435478070939 3459382 71.3229636280733 951400000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_other | ||
| 2C 51 138.4557981025427 2739034 70.04883428088044 758300000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_other | ||
| 6A 51.5 138.16988709079544 3695890 72.83153253863364 1021000000 pass/pass warn/fail warn/pass fail/warn warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_other | ||
| 6C 51 136.6471336176722 2978371 69.02758056587716 813800000 pass/pass warn/fail warn/warn fail/warn warn/pass pass/pass warn/warn fail/fail fail/warn pass/pass remove_other | ||
| SS1 51 137.25906460305947 4919024 64.38974910989987 1350100000 pass/pass warn/fail warn/warn fail/warn pass/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_other | ||
| SS2 50 136.9208956401317 3016926 58.67105264083944 826000000 pass/pass warn/fail warn/warn fail/fail warn/pass pass/pass warn/warn fail/fail warn/warn pass/pass remove_other |
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