Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_1W6-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_1W6-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_1W6-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1W6-N1-BDNA-1_A23MHW3LT4_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: 56767834 total, 39134 skipped (flags/unmapped)
Fragments: 28539191 total (28164463 tlen-paired, 2093 hash-paired, 268 singletons, 9835 discordant, 362532 orphans, 6559 too large [>5000 bp], 8994394 duplicates)
Reads: 60191064 total, 36114 skipped (flags/unmapped)
Fragments: 30261142 total (29864745 tlen-paired, 3570 hash-paired, 230 singletons, 8095 discordant, 384502 orphans, 8699 too large [>5000 bp], 9547812 duplicates)
Reads: 60821772 total, 35632 skipped (flags/unmapped)
Fragments: 30577391 total (30183761 tlen-paired, 2293 hash-paired, 393 singletons, 7069 discordant, 383875 orphans, 7813 too large [>5000 bp], 9358866 duplicates)
Reads: 67157037 total, 61172 skipped (flags/unmapped)
Fragments: 33941291 total (32696486 tlen-paired, 1568 hash-paired, 276 singletons, 251210 discordant, 991751 orphans, 102655 too large [>5000 bp], 10666294 duplicates)