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: 1029_I46-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_I46-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I46-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I46-N1-BDNA-1_B23MHTGLT4_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: 70328502 total, 53860 skipped (flags/unmapped)
Fragments: 35339525 total (34901298 tlen-paired, 2876 hash-paired, 372 singletons, 13701 discordant, 421278 orphans, 8621 too large [>5000 bp], 11389904 duplicates)
Reads: 74793888 total, 46229 skipped (flags/unmapped)
Fragments: 37584128 total (37130781 tlen-paired, 2703 hash-paired, 480 singletons, 9563 discordant, 440601 orphans, 10242 too large [>5000 bp], 11859455 duplicates)
Reads: 82676749 total, 85229 skipped (flags/unmapped)
Fragments: 41749555 total (40331330 tlen-paired, 2540 hash-paired, 466 singletons, 277693 discordant, 1137526 orphans, 115201 too large [>5000 bp], 13407301 duplicates)
Reads: 81331764 total, 52006 skipped (flags/unmapped)
Fragments: 40870522 total (40348630 tlen-paired, 4290 hash-paired, 401 singletons, 13884 discordant, 503317 orphans, 21216 too large [>5000 bp], 13197192 duplicates)