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_BNFE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BNFE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BNFE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_BNFE-N1-BDNA-1_A23TY32LT4_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: 98152740 total, 52403 skipped (flags/unmapped)
Fragments: 49205335 total (48861418 tlen-paired, 2779 hash-paired, 416 singletons, 10117 discordant, 330605 orphans, 10344 too large [>5000 bp], 19256407 duplicates)
Reads: 97517705 total, 56428 skipped (flags/unmapped)
Fragments: 48889443 total (48517515 tlen-paired, 4785 hash-paired, 333 singletons, 12182 discordant, 354628 orphans, 18676 too large [>5000 bp], 19548783 duplicates)
Reads: 90600636 total, 61669 skipped (flags/unmapped)
Fragments: 45415458 total (45085913 tlen-paired, 4297 hash-paired, 446 singletons, 13865 discordant, 310937 orphans, 9717 too large [>5000 bp], 18082625 duplicates)
Reads: 107913038 total, 98481 skipped (flags/unmapped)
Fragments: 54217265 total (53245699 tlen-paired, 3288 hash-paired, 376 singletons, 192729 discordant, 775173 orphans, 77788 too large [>5000 bp], 21664783 duplicates)