Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1267_C1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1267_C1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1267_C1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_C1-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 89044729 total, 60977 skipped (flags/unmapped)
Fragments: 44615697 total (44327806 tlen-paired, 4186 hash-paired, 419 singletons, 13645 discordant, 269641 orphans, 11209 too large [>5000 bp], 16006445 duplicates)
Reads: 95832501 total, 55353 skipped (flags/unmapped)
Fragments: 48020583 total (47721488 tlen-paired, 4359 hash-paired, 483 singletons, 9284 discordant, 284969 orphans, 10717 too large [>5000 bp], 16932857 duplicates)
Reads: 104133991 total, 55974 skipped (flags/unmapped)
Fragments: 52182340 total (51835578 tlen-paired, 6597 hash-paired, 363 singletons, 13596 discordant, 326206 orphans, 19953 too large [>5000 bp], 18813553 duplicates)
Reads: 105087138 total, 95238 skipped (flags/unmapped)
Fragments: 52762873 total (51941396 tlen-paired, 4051 hash-paired, 454 singletons, 157316 discordant, 659656 orphans, 63132 too large [>5000 bp], 19055020 duplicates)