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_G74-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_G74-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G74-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G74-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: 74984636 total, 53394 skipped (flags/unmapped)
Fragments: 37581540 total (37308649 tlen-paired, 3653 hash-paired, 387 singletons, 15936 discordant, 252915 orphans, 10732 too large [>5000 bp], 14474602 duplicates)
Reads: 80489202 total, 41961 skipped (flags/unmapped)
Fragments: 40342205 total (40075256 tlen-paired, 2047 hash-paired, 388 singletons, 10251 discordant, 254263 orphans, 8741 too large [>5000 bp], 15240566 duplicates)
Reads: 88612409 total, 47533 skipped (flags/unmapped)
Fragments: 44415044 total (44096596 tlen-paired, 3986 hash-paired, 317 singletons, 15224 discordant, 298921 orphans, 17013 too large [>5000 bp], 17183299 duplicates)
Reads: 88944120 total, 72649 skipped (flags/unmapped)
Fragments: 44659288 total (43966365 tlen-paired, 2752 hash-paired, 341 singletons, 130386 discordant, 559444 orphans, 56340 too large [>5000 bp], 17338331 duplicates)