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_dEm-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 659_dEm-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dEm-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dEm-N1-BDNA-1_B23L5TMLT4_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: 65167550 total, 61427 skipped (flags/unmapped)
Fragments: 32697423 total (32371879 tlen-paired, 4613 hash-paired, 430 singletons, 15172 discordant, 305329 orphans, 8518 too large [>5000 bp], 11557476 duplicates)
Reads: 69391587 total, 51435 skipped (flags/unmapped)
Fragments: 34815556 total (34489856 tlen-paired, 2931 hash-paired, 457 singletons, 10023 discordant, 312289 orphans, 10893 too large [>5000 bp], 12108086 duplicates)
Reads: 76728108 total, 93893 skipped (flags/unmapped)
Fragments: 38616385 total (37686757 tlen-paired, 5273 hash-paired, 451 singletons, 177314 discordant, 746590 orphans, 74243 too large [>5000 bp], 13663105 duplicates)
Reads: 76396389 total, 54919 skipped (flags/unmapped)
Fragments: 38333448 total (37948270 tlen-paired, 5327 hash-paired, 383 singletons, 15203 discordant, 364265 orphans, 19611 too large [>5000 bp], 13638613 duplicates)