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_dCI-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dCI-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 659_dCI-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dCI-N1-BDNA-1_A23TY32LT4_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: 75179217 total, 62471 skipped (flags/unmapped)
Fragments: 37692183 total (37388632 tlen-paired, 4531 hash-paired, 359 singletons, 11892 discordant, 286769 orphans, 9754 too large [>5000 bp], 14587990 duplicates)
Reads: 80382851 total, 48344 skipped (flags/unmapped)
Fragments: 40307601 total (39998155 tlen-paired, 2786 hash-paired, 366 singletons, 7791 discordant, 298503 orphans, 9087 too large [>5000 bp], 15445274 duplicates)
Reads: 88015784 total, 52992 skipped (flags/unmapped)
Fragments: 44138456 total (43780027 tlen-paired, 4901 hash-paired, 303 singletons, 11686 discordant, 341539 orphans, 13861 too large [>5000 bp], 17223988 duplicates)
Reads: 89454872 total, 96669 skipped (flags/unmapped)
Fragments: 44973993 total (44051550 tlen-paired, 4124 hash-paired, 300 singletons, 180012 discordant, 738007 orphans, 74262 too large [>5000 bp], 17498104 duplicates)