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: 1241_R9U-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R9U-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R9U-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R9U-N1-BDNA-1_A23TY7KLT4_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: 83925246 total, 59955 skipped (flags/unmapped)
Fragments: 42057894 total (41768367 tlen-paired, 2793 hash-paired, 282 singletons, 14443 discordant, 272009 orphans, 10897 too large [>5000 bp], 14138822 duplicates)
Reads: 89465583 total, 48584 skipped (flags/unmapped)
Fragments: 44836256 total (44549086 tlen-paired, 2853 hash-paired, 374 singletons, 9468 discordant, 274475 orphans, 9668 too large [>5000 bp], 14926828 duplicates)
Reads: 98127521 total, 85617 skipped (flags/unmapped)
Fragments: 49279514 total (48481610 tlen-paired, 2003 hash-paired, 347 singletons, 151103 discordant, 644451 orphans, 63837 too large [>5000 bp], 16776464 duplicates)
Reads: 97705723 total, 56073 skipped (flags/unmapped)
Fragments: 48971041 total (48610078 tlen-paired, 6785 hash-paired, 338 singletons, 14504 discordant, 339336 orphans, 23621 too large [>5000 bp], 16626318 duplicates)