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: 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BAE3-N1-BDNA-1_B23KGCJLT4_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: 80190414 total, 59313 skipped (flags/unmapped)
Fragments: 40160539 total (39924536 tlen-paired, 3447 hash-paired, 401 singletons, 15519 discordant, 216636 orphans, 13530 too large [>5000 bp], 16040214 duplicates)
Reads: 84591884 total, 44531 skipped (flags/unmapped)
Fragments: 42369584 total (42145833 tlen-paired, 2548 hash-paired, 354 singletons, 10674 discordant, 210175 orphans, 9357 too large [>5000 bp], 16656992 duplicates)
Reads: 94260257 total, 77393 skipped (flags/unmapped)
Fragments: 47266808 total (46732204 tlen-paired, 2672 hash-paired, 353 singletons, 97466 discordant, 434113 orphans, 41857 too large [>5000 bp], 19113128 duplicates)
Reads: 93991743 total, 50381 skipped (flags/unmapped)
Fragments: 47080624 total (46791208 tlen-paired, 4990 hash-paired, 306 singletons, 15922 discordant, 268198 orphans, 24309 too large [>5000 bp], 18947847 duplicates)