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_BICJ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BICJ-N1-BDNA-1_B23KGCJLT4_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: 81065878 total, 55563 skipped (flags/unmapped)
Fragments: 40613924 total (40356790 tlen-paired, 4069 hash-paired, 415 singletons, 13390 discordant, 239260 orphans, 11071 too large [>5000 bp], 15238485 duplicates)
Reads: 86528459 total, 48340 skipped (flags/unmapped)
Fragments: 43350805 total (43094285 tlen-paired, 3748 hash-paired, 476 singletons, 9551 discordant, 242745 orphans, 10865 too large [>5000 bp], 16055551 duplicates)
Reads: 95915247 total, 74391 skipped (flags/unmapped)
Fragments: 48138170 total (47467311 tlen-paired, 1815 hash-paired, 389 singletons, 126070 discordant, 542585 orphans, 53745 too large [>5000 bp], 18216590 duplicates)
Reads: 95534654 total, 49562 skipped (flags/unmapped)
Fragments: 47865541 total (47571645 tlen-paired, 3573 hash-paired, 265 singletons, 13487 discordant, 276571 orphans, 15423 too large [>5000 bp], 18084110 duplicates)