Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_05Q-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_05Q-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
[W::hts_idx_load3] The index file is older than the data file: 1136_05Q-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_05Q-N1-BDNA-1_A23MHW3LT4_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: 73556176 total, 47798 skipped (flags/unmapped)
Fragments: 36958085 total (36519522 tlen-paired, 2205 hash-paired, 531 singletons, 9730 discordant, 426097 orphans, 9418 too large [>5000 bp], 12118166 duplicates)
Reads: 80476804 total, 53735 skipped (flags/unmapped)
Fragments: 40437431 total (39924297 tlen-paired, 5015 hash-paired, 482 singletons, 14812 discordant, 492825 orphans, 20757 too large [>5000 bp], 13605669 duplicates)
Reads: 81552748 total, 89648 skipped (flags/unmapped)
Fragments: 41169454 total (39798753 tlen-paired, 2154 hash-paired, 481 singletons, 265903 discordant, 1102163 orphans, 113418 too large [>5000 bp], 13804089 duplicates)
Reads: 69558342 total, 55713 skipped (flags/unmapped)
Fragments: 34950863 total (34515662 tlen-paired, 2284 hash-paired, 525 singletons, 14328 discordant, 418064 orphans, 9746 too large [>5000 bp], 11718635 duplicates)