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_SHN-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_SHN-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_SHN-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_SHN-N1-BDNA-1_A23TY7KLT4_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: 71560785 total, 40602 skipped (flags/unmapped)
Fragments: 35848024 total (35646396 tlen-paired, 2528 hash-paired, 344 singletons, 7539 discordant, 191217 orphans, 7848 too large [>5000 bp], 12624152 duplicates)
Reads: 66552266 total, 49352 skipped (flags/unmapped)
Fragments: 33336603 total (33134882 tlen-paired, 3235 hash-paired, 294 singletons, 11034 discordant, 187158 orphans, 8580 too large [>5000 bp], 11977892 duplicates)
Reads: 70872733 total, 44641 skipped (flags/unmapped)
Fragments: 35507164 total (35282216 tlen-paired, 4371 hash-paired, 271 singletons, 9253 discordant, 211053 orphans, 12544 too large [>5000 bp], 12814580 duplicates)
Reads: 77511815 total, 74013 skipped (flags/unmapped)
Fragments: 38886199 total (38363548 tlen-paired, 2633 hash-paired, 322 singletons, 99862 discordant, 419834 orphans, 42780 too large [>5000 bp], 14104710 duplicates)