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_BPDR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BPDR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_BPDR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BPDR-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: 51869839 total, 33748 skipped (flags/unmapped)
Fragments: 26018514 total (25797383 tlen-paired, 1671 hash-paired, 265 singletons, 7729 discordant, 211466 orphans, 5397 too large [>5000 bp], 9548934 duplicates)
Reads: 55983329 total, 30963 skipped (flags/unmapped)
Fragments: 28087455 total (27846967 tlen-paired, 1546 hash-paired, 285 singletons, 5532 discordant, 233125 orphans, 5433 too large [>5000 bp], 10031781 duplicates)
Reads: 56047559 total, 31355 skipped (flags/unmapped)
Fragments: 28117265 total (27864516 tlen-paired, 2525 hash-paired, 202 singletons, 6844 discordant, 243178 orphans, 12527 too large [>5000 bp], 10300541 duplicates)
Reads: 62332626 total, 55885 skipped (flags/unmapped)
Fragments: 31365176 total (30653952 tlen-paired, 2391 hash-paired, 268 singletons, 144094 discordant, 564471 orphans, 55564 too large [>5000 bp], 11473591 duplicates)