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: 1029_BOHJ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BOHJ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BOHJ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BOHJ-N1-BDNA-1_235YY7LT3_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: 57209690 total, 42996 skipped (flags/unmapped)
Fragments: 28722735 total (28420157 tlen-paired, 2832 hash-paired, 3335 singletons, 5930 discordant, 290481 orphans, 7520 too large [>5000 bp], 6424715 duplicates)
Reads: 53826614 total, 46368 skipped (flags/unmapped)
Fragments: 27025189 total (26735766 tlen-paired, 2924 hash-paired, 3230 singletons, 8509 discordant, 274760 orphans, 3929 too large [>5000 bp], 6171865 duplicates)
Reads: 59194169 total, 45097 skipped (flags/unmapped)
Fragments: 29719044 total (29391498 tlen-paired, 2540 hash-paired, 3483 singletons, 8554 discordant, 312969 orphans, 13718 too large [>5000 bp], 6697848 duplicates)
Reads: 59905638 total, 69092 skipped (flags/unmapped)
Fragments: 30216584 total (29296212 tlen-paired, 2191 hash-paired, 3540 singletons, 175733 discordant, 738908 orphans, 72913 too large [>5000 bp], 6776501 duplicates)