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_D89-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_D89-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_D89-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1241_D89-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: 96991527 total, 72147 skipped (flags/unmapped)
Fragments: 48583071 total (48286017 tlen-paired, 4351 hash-paired, 341 singletons, 16181 discordant, 276181 orphans, 14880 too large [>5000 bp], 17830791 duplicates)
Reads: 102298513 total, 60467 skipped (flags/unmapped)
Fragments: 51251818 total (50914891 tlen-paired, 6133 hash-paired, 304 singletons, 13792 discordant, 316698 orphans, 25706 too large [>5000 bp], 18991888 duplicates)
Reads: 103554983 total, 54066 skipped (flags/unmapped)
Fragments: 51880120 total (51586388 tlen-paired, 2331 hash-paired, 489 singletons, 11470 discordant, 279442 orphans, 10304 too large [>5000 bp], 18801247 duplicates)
Reads: 112902362 total, 98693 skipped (flags/unmapped)
Fragments: 56644967 total (55886921 tlen-paired, 3169 hash-paired, 396 singletons, 144772 discordant, 609709 orphans, 61920 too large [>5000 bp], 20996285 duplicates)