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_SH1-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_SH1-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_SH1-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_SH1-N1-BDNA-1_A23KFG7LT4_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: 71193762 total, 46904 skipped (flags/unmapped)
Fragments: 35676944 total (35438873 tlen-paired, 3542 hash-paired, 414 singletons, 11297 discordant, 222818 orphans, 8101 too large [>5000 bp], 11756378 duplicates)
Reads: 75943934 total, 42078 skipped (flags/unmapped)
Fragments: 38062149 total (37795907 tlen-paired, 2664 hash-paired, 267 singletons, 9426 discordant, 253885 orphans, 15855 too large [>5000 bp], 12551779 duplicates)
Reads: 76775984 total, 40230 skipped (flags/unmapped)
Fragments: 38476813 total (38230189 tlen-paired, 2919 hash-paired, 341 singletons, 7963 discordant, 235401 orphans, 8935 too large [>5000 bp], 12302364 duplicates)
Reads: 84071815 total, 71474 skipped (flags/unmapped)
Fragments: 42213374 total (41544473 tlen-paired, 3301 hash-paired, 330 singletons, 131257 discordant, 534013 orphans, 53968 too large [>5000 bp], 13951267 duplicates)