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_B215-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B215-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_B215-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B215-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: 92160931 total, 61689 skipped (flags/unmapped)
Fragments: 46212700 total (45849710 tlen-paired, 3083 hash-paired, 511 singletons, 13309 discordant, 346087 orphans, 10220 too large [>5000 bp], 16944010 duplicates)
Reads: 98766429 total, 52879 skipped (flags/unmapped)
Fragments: 49532461 total (49150523 tlen-paired, 2449 hash-paired, 531 singletons, 9475 discordant, 369483 orphans, 9321 too large [>5000 bp], 17795543 duplicates)
Reads: 107836400 total, 55914 skipped (flags/unmapped)
Fragments: 54079511 total (53643907 tlen-paired, 4805 hash-paired, 439 singletons, 13311 discordant, 417049 orphans, 19476 too large [>5000 bp], 19929044 duplicates)
Reads: 110179589 total, 97186 skipped (flags/unmapped)
Fragments: 55410149 total (54264109 tlen-paired, 3218 hash-paired, 444 singletons, 226759 discordant, 915619 orphans, 89084 too large [>5000 bp], 20392239 duplicates)