Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3S1-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_3S1-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3S1-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3S1-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: 67976451 total, 50770 skipped (flags/unmapped)
Fragments: 34082965 total (33806383 tlen-paired, 2751 hash-paired, 353 singletons, 12772 discordant, 260706 orphans, 10405 too large [>5000 bp], 12993343 duplicates)
Reads: 72619698 total, 43430 skipped (flags/unmapped)
Fragments: 36425404 total (36109342 tlen-paired, 2757 hash-paired, 269 singletons, 11413 discordant, 301623 orphans, 13676 too large [>5000 bp], 13877038 duplicates)
Reads: 72902787 total, 41489 skipped (flags/unmapped)
Fragments: 36556672 total (36274318 tlen-paired, 2562 hash-paired, 390 singletons, 9508 discordant, 269894 orphans, 9119 too large [>5000 bp], 13562144 duplicates)
Reads: 80481885 total, 68790 skipped (flags/unmapped)
Fragments: 40451016 total (39686015 tlen-paired, 2369 hash-paired, 280 singletons, 149815 discordant, 612537 orphans, 61940 too large [>5000 bp], 15408950 duplicates)