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: 1029_3YY-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_3YY-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_3YY-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] 
The index file is older than the data file: 1029_3YY-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: 88886072 total, 75931 skipped (flags/unmapped)
Fragments: 44673430 total (44093407 tlen-paired, 3808 hash-paired, 587 singletons, 15998 discordant, 559630 orphans, 11749 too large [>5000 bp], 17003074 duplicates)
Reads: 93729051 total, 63851 skipped (flags/unmapped)
Fragments: 47109505 total (46516192 tlen-paired, 3194 hash-paired, 515 singletons, 10941 discordant, 578663 orphans, 12684 too large [>5000 bp], 17616108 duplicates)
Reads: 102834282 total, 70601 skipped (flags/unmapped)
Fragments: 51683697 total (51007847 tlen-paired, 6572 hash-paired, 537 singletons, 16009 discordant, 652732 orphans, 24778 too large [>5000 bp], 19709300 duplicates)
Reads: 104547414 total, 117123 skipped (flags/unmapped)
Fragments: 52823094 total (50911658 tlen-paired, 2744 hash-paired, 548 singletons, 376191 discordant, 1531953 orphans, 158302 too large [>5000 bp], 19971098 duplicates)