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_BHCY-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BHCY-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_BHCY-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BHCY-N1-BDNA-1_A23TNVNLT4_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: 97230898 total, 64498 skipped (flags/unmapped)
Fragments: 48736439 total (48388870 tlen-paired, 3525 hash-paired, 406 singletons, 16500 discordant, 327138 orphans, 10533 too large [>5000 bp], 17454067 duplicates)
Reads: 104538961 total, 52724 skipped (flags/unmapped)
Fragments: 52403338 total (52048086 tlen-paired, 2866 hash-paired, 524 singletons, 11637 discordant, 340225 orphans, 10155 too large [>5000 bp], 18476542 duplicates)
Reads: 114445334 total, 61140 skipped (flags/unmapped)
Fragments: 57368189 total (56949584 tlen-paired, 5712 hash-paired, 418 singletons, 17165 discordant, 395310 orphans, 21772 too large [>5000 bp], 20767779 duplicates)
Reads: 116071853 total, 102770 skipped (flags/unmapped)
Fragments: 58305190 total (57316230 tlen-paired, 2744 hash-paired, 488 singletons, 191361 discordant, 794367 orphans, 76779 too large [>5000 bp], 21119775 duplicates)