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_Yr-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
[W::hts_idx_load3] The index file is older than the data file: 659_Yr-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_Yr-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Yr-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: 69642428 total, 54094 skipped (flags/unmapped)
Fragments: 34932426 total (34619351 tlen-paired, 4223 hash-paired, 352 singletons, 11570 discordant, 296930 orphans, 10382 too large [>5000 bp], 12874519 duplicates)
Reads: 73891224 total, 45368 skipped (flags/unmapped)
Fragments: 37068085 total (36750969 tlen-paired, 2890 hash-paired, 462 singletons, 7930 discordant, 305834 orphans, 7991 too large [>5000 bp], 13450831 duplicates)
Reads: 81775489 total, 85677 skipped (flags/unmapped)
Fragments: 41150702 total (40193477 tlen-paired, 3272 hash-paired, 394 singletons, 185669 discordant, 767890 orphans, 78346 too large [>5000 bp], 15188225 duplicates)
Reads: 80636843 total, 49945 skipped (flags/unmapped)
Fragments: 40455988 total (40077053 tlen-paired, 4670 hash-paired, 339 singletons, 11417 discordant, 362509 orphans, 18885 too large [>5000 bp], 14969486 duplicates)