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: 659_bmI-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bmI-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bmI-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 659_bmI-N1-BDNA-1_B23H3Y2LT3_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: 75363692 total, 62209 skipped (flags/unmapped)
Fragments: 37894197 total (37376023 tlen-paired, 10155 hash-paired, 2885 singletons, 5106 discordant, 500028 orphans, 8001 too large [>5000 bp], 7676356 duplicates)
Reads: 68815399 total, 75294 skipped (flags/unmapped)
Fragments: 34586201 total (34120331 tlen-paired, 10079 hash-paired, 2616 singletons, 7248 discordant, 445927 orphans, 8123 too large [>5000 bp], 7030821 duplicates)
Reads: 69067204 total, 63331 skipped (flags/unmapped)
Fragments: 34724752 total (34229793 tlen-paired, 11225 hash-paired, 2555 singletons, 6801 discordant, 474378 orphans, 15651 too large [>5000 bp], 7009000 duplicates)
Reads: 78295674 total, 166130 skipped (flags/unmapped)
Fragments: 39584132 total (37945513 tlen-paired, 11796 hash-paired, 3035 singletons, 326085 discordant, 1297703 orphans, 131009 too large [>5000 bp], 7894088 duplicates)