Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3BO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3BO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_3BO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3BO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 91895347 total, 64054 skipped (flags/unmapped)
Fragments: 46184253 total (45601630 tlen-paired, 3560 hash-paired, 454 singletons, 19918 discordant, 558691 orphans, 10966 too large [>5000 bp], 18106574 duplicates)
Reads: 98773932 total, 54490 skipped (flags/unmapped)
Fragments: 49642402 total (49036294 tlen-paired, 2438 hash-paired, 585 singletons, 14502 discordant, 588583 orphans, 11903 too large [>5000 bp], 18919877 duplicates)
Reads: 98053874 total, 58342 skipped (flags/unmapped)
Fragments: 49283107 total (48649051 tlen-paired, 4083 hash-paired, 430 singletons, 17045 discordant, 612498 orphans, 21123 too large [>5000 bp], 19330582 duplicates)
Reads: 109097493 total, 97049 skipped (flags/unmapped)
Fragments: 55076274 total (53256429 tlen-paired, 3970 hash-paired, 489 singletons, 364487 discordant, 1450899 orphans, 149642 too large [>5000 bp], 21531837 duplicates)