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_BCKB-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BCKB-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCKB-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCKB-N1-BDNA-1_B23KFG5LT4_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: 88705371 total, 65818 skipped (flags/unmapped)
Fragments: 44463883 total (44126541 tlen-paired, 4564 hash-paired, 388 singletons, 17911 discordant, 314479 orphans, 13327 too large [>5000 bp], 18922980 duplicates)
Reads: 94839216 total, 56594 skipped (flags/unmapped)
Fragments: 47545322 total (47164141 tlen-paired, 2627 hash-paired, 318 singletons, 15562 discordant, 362674 orphans, 27485 too large [>5000 bp], 20305594 duplicates)
Reads: 94843406 total, 55800 skipped (flags/unmapped)
Fragments: 47541814 total (47203885 tlen-paired, 3667 hash-paired, 467 singletons, 12174 discordant, 321621 orphans, 13033 too large [>5000 bp], 19840357 duplicates)
Reads: 104494695 total, 95715 skipped (flags/unmapped)
Fragments: 52479785 total (51601256 tlen-paired, 3229 hash-paired, 375 singletons, 169828 discordant, 705097 orphans, 72441 too large [>5000 bp], 22414883 duplicates)