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_BR5R-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_BR5R-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BR5R-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BR5R-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: 83118578 total, 62872 skipped (flags/unmapped)
Fragments: 41647796 total (41372272 tlen-paired, 3299 hash-paired, 329 singletons, 12871 discordant, 259025 orphans, 9734 too large [>5000 bp], 14747376 duplicates)
Reads: 89236930 total, 53429 skipped (flags/unmapped)
Fragments: 44718750 total (44419572 tlen-paired, 3254 hash-paired, 251 singletons, 11389 discordant, 284284 orphans, 15268 too large [>5000 bp], 15947284 duplicates)
Reads: 90065032 total, 52635 skipped (flags/unmapped)
Fragments: 45130674 total (44848503 tlen-paired, 3054 hash-paired, 430 singletons, 8992 discordant, 269695 orphans, 10587 too large [>5000 bp], 15676054 duplicates)
Reads: 98017153 total, 92379 skipped (flags/unmapped)
Fragments: 49206873 total (48438781 tlen-paired, 3634 hash-paired, 358 singletons, 149840 discordant, 614260 orphans, 62823 too large [>5000 bp], 17558207 duplicates)