Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_HE1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_HE1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_HE1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_HE1-N1-BDNA-1_A23NLN3LT4_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: 82187705 total, 57948 skipped (flags/unmapped)
Fragments: 41176032 total (40915637 tlen-paired, 3566 hash-paired, 412 singletons, 12792 discordant, 243625 orphans, 10865 too large [>5000 bp], 14397117 duplicates)
Reads: 87543312 total, 45464 skipped (flags/unmapped)
Fragments: 43864540 total (43601777 tlen-paired, 2788 hash-paired, 363 singletons, 8809 discordant, 250803 orphans, 9967 too large [>5000 bp], 15004427 duplicates)
Reads: 96360888 total, 51587 skipped (flags/unmapped)
Fragments: 48288084 total (47965498 tlen-paired, 4183 hash-paired, 351 singletons, 13202 discordant, 304850 orphans, 19167 too large [>5000 bp], 16933860 duplicates)
Reads: 96764946 total, 83191 skipped (flags/unmapped)
Fragments: 48571256 total (47861313 tlen-paired, 2481 hash-paired, 351 singletons, 133839 discordant, 573272 orphans, 56433 too large [>5000 bp], 17074288 duplicates)