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_BQ3K-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_BQ3K-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BQ3K-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BQ3K-N1-BDNA-1_B23H2GYLT3_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: 84519737 total, 64151 skipped (flags/unmapped)
Fragments: 42470917 total (41934989 tlen-paired, 15496 hash-paired, 6261 singletons, 8456 discordant, 505715 orphans, 12864 too large [>5000 bp], 8997163 duplicates)
Reads: 93244171 total, 66849 skipped (flags/unmapped)
Fragments: 46862657 total (46270028 tlen-paired, 16072 hash-paired, 6950 singletons, 7307 discordant, 562300 orphans, 10629 too large [>5000 bp], 9910882 duplicates)
Reads: 83827525 total, 73807 skipped (flags/unmapped)
Fragments: 42111033 total (41600296 tlen-paired, 16195 hash-paired, 6595 singletons, 9540 discordant, 478407 orphans, 8327 too large [>5000 bp], 8981730 duplicates)
Reads: 94923396 total, 116434 skipped (flags/unmapped)
Fragments: 47973977 total (46202265 tlen-paired, 18100 hash-paired, 7304 singletons, 349174 discordant, 1397134 orphans, 131723 too large [>5000 bp], 10042665 duplicates)