Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_GHR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GHR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GHR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_GHR-N1-BDNA-1_A23NLN3LT4_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: 86949325 total, 62494 skipped (flags/unmapped)
Fragments: 43575812 total (43267388 tlen-paired, 3533 hash-paired, 401 singletons, 17054 discordant, 287436 orphans, 11522 too large [>5000 bp], 15379015 duplicates)
Reads: 92689002 total, 55137 skipped (flags/unmapped)
Fragments: 46452847 total (46142533 tlen-paired, 2858 hash-paired, 517 singletons, 11669 discordant, 295270 orphans, 11979 too large [>5000 bp], 16129847 duplicates)
Reads: 101852644 total, 56782 skipped (flags/unmapped)
Fragments: 51050120 total (50677612 tlen-paired, 5135 hash-paired, 368 singletons, 16807 discordant, 350198 orphans, 23094 too large [>5000 bp], 18140375 duplicates)
Reads: 102358178 total, 92776 skipped (flags/unmapped)
Fragments: 51397861 total (50585341 tlen-paired, 2907 hash-paired, 374 singletons, 153065 discordant, 656174 orphans, 63114 too large [>5000 bp], 18314529 duplicates)