Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_JH4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JH4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_JH4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JH4-N1-BDNA-1_A23TNVNLT4_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: 80883577 total, 54712 skipped (flags/unmapped)
Fragments: 40553907 total (40235695 tlen-paired, 3128 hash-paired, 354 singletons, 16229 discordant, 298501 orphans, 9953 too large [>5000 bp], 15157855 duplicates)
Reads: 87023061 total, 47151 skipped (flags/unmapped)
Fragments: 43632632 total (43310849 tlen-paired, 2705 hash-paired, 459 singletons, 11304 discordant, 307315 orphans, 9210 too large [>5000 bp], 15953587 duplicates)
Reads: 86642275 total, 48759 skipped (flags/unmapped)
Fragments: 43445018 total (43093906 tlen-paired, 3422 hash-paired, 343 singletons, 14102 discordant, 333245 orphans, 18534 too large [>5000 bp], 16318316 duplicates)
Reads: 95838613 total, 86981 skipped (flags/unmapped)
Fragments: 48154912 total (47287809 tlen-paired, 3212 hash-paired, 390 singletons, 168699 discordant, 694802 orphans, 68500 too large [>5000 bp], 18122112 duplicates)