Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_1UW-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_1UW-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_1UW-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_1UW-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: 81862499 total, 60009 skipped (flags/unmapped)
Fragments: 41031722 total (40727419 tlen-paired, 3694 hash-paired, 362 singletons, 15699 discordant, 284548 orphans, 11978 too large [>5000 bp], 14545190 duplicates)
Reads: 87706901 total, 51767 skipped (flags/unmapped)
Fragments: 43968898 total (43639042 tlen-paired, 2836 hash-paired, 330 singletons, 13402 discordant, 313288 orphans, 15478 too large [>5000 bp], 15717119 duplicates)
Reads: 88240732 total, 51790 skipped (flags/unmapped)
Fragments: 44229999 total (43920964 tlen-paired, 2722 hash-paired, 412 singletons, 11391 discordant, 294510 orphans, 11933 too large [>5000 bp], 15360859 duplicates)
Reads: 96805186 total, 84592 skipped (flags/unmapped)
Fragments: 48623246 total (47809174 tlen-paired, 2986 hash-paired, 374 singletons, 157708 discordant, 653004 orphans, 63740 too large [>5000 bp], 17385981 duplicates)