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: 1029_BKQJ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BKQJ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BKQJ-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BKQJ-N1-BDNA-1_A23KFG7LT4_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: 53485581 total, 37835 skipped (flags/unmapped)
Fragments: 26890526 total (26528934 tlen-paired, 2121 hash-paired, 283 singletons, 8643 discordant, 350545 orphans, 8761 too large [>5000 bp], 9737735 duplicates)
Reads: 56999848 total, 32303 skipped (flags/unmapped)
Fragments: 28662749 total (28280829 tlen-paired, 1801 hash-paired, 328 singletons, 6726 discordant, 373065 orphans, 7720 too large [>5000 bp], 10028906 duplicates)
Reads: 56902496 total, 32472 skipped (flags/unmapped)
Fragments: 28613666 total (28214348 tlen-paired, 1855 hash-paired, 217 singletons, 7765 discordant, 389481 orphans, 16195 too large [>5000 bp], 10321919 duplicates)
Reads: 63526923 total, 48333 skipped (flags/unmapped)
Fragments: 32121820 total (30902381 tlen-paired, 2274 hash-paired, 289 singletons, 246775 discordant, 970101 orphans, 102670 too large [>5000 bp], 11543593 duplicates)