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_JM9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JM9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_JM9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JM9-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: 81939925 total, 61354 skipped (flags/unmapped)
Fragments: 41145182 total (40695922 tlen-paired, 3191 hash-paired, 385 singletons, 12020 discordant, 433664 orphans, 11128 too large [>5000 bp], 18171044 duplicates)
Reads: 88093485 total, 54126 skipped (flags/unmapped)
Fragments: 44244017 total (43763840 tlen-paired, 3307 hash-paired, 512 singletons, 8631 discordant, 467727 orphans, 9782 too large [>5000 bp], 19243572 duplicates)
Reads: 97296915 total, 58832 skipped (flags/unmapped)
Fragments: 48862104 total (48307584 tlen-paired, 3896 hash-paired, 298 singletons, 12553 discordant, 537773 orphans, 25973 too large [>5000 bp], 21658623 duplicates)
Reads: 99119247 total, 109784 skipped (flags/unmapped)
Fragments: 49992042 total (48454636 tlen-paired, 3887 hash-paired, 388 singletons, 308252 discordant, 1224879 orphans, 125323 too large [>5000 bp], 21995675 duplicates)