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_BG4W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_BG4W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BG4W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BG4W-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: 74132857 total, 54666 skipped (flags/unmapped)
Fragments: 37155452 total (36890521 tlen-paired, 3408 hash-paired, 357 singletons, 11738 discordant, 249428 orphans, 8536 too large [>5000 bp], 13088282 duplicates)
Reads: 79577483 total, 44746 skipped (flags/unmapped)
Fragments: 39888760 total (39617194 tlen-paired, 1873 hash-paired, 386 singletons, 8482 discordant, 260825 orphans, 8214 too large [>5000 bp], 13732718 duplicates)
Reads: 78794930 total, 46929 skipped (flags/unmapped)
Fragments: 39498782 total (39199934 tlen-paired, 5184 hash-paired, 213 singletons, 10625 discordant, 282826 orphans, 16738 too large [>5000 bp], 13972689 duplicates)
Reads: 87050280 total, 79919 skipped (flags/unmapped)
Fragments: 43723310 total (42975524 tlen-paired, 2949 hash-paired, 301 singletons, 146510 discordant, 598026 orphans, 61034 too large [>5000 bp], 15449217 duplicates)