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_QPE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_QPE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_QPE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_QPE-N1-BDNA-1_A23TY32LT4_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: 68350772 total, 41218 skipped (flags/unmapped)
Fragments: 34267770 total (34015579 tlen-paired, 2799 hash-paired, 334 singletons, 7736 discordant, 241322 orphans, 7835 too large [>5000 bp], 12331653 duplicates)
Reads: 63600127 total, 48521 skipped (flags/unmapped)
Fragments: 31884198 total (31637595 tlen-paired, 2713 hash-paired, 306 singletons, 11344 discordant, 232240 orphans, 7878 too large [>5000 bp], 11589117 duplicates)
Reads: 75076170 total, 46359 skipped (flags/unmapped)
Fragments: 37640304 total (37344501 tlen-paired, 4429 hash-paired, 254 singletons, 11683 discordant, 279437 orphans, 14447 too large [>5000 bp], 13760412 duplicates)
Reads: 75866492 total, 76596 skipped (flags/unmapped)
Fragments: 38124120 total (37412791 tlen-paired, 2665 hash-paired, 286 singletons, 138338 discordant, 570040 orphans, 55991 too large [>5000 bp], 13909752 duplicates)