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_LMJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_LMJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_LMJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

The index file is older than the data file: 1029_LMJ-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: 70887255 total, 51123 skipped (flags/unmapped)
Fragments: 35600237 total (35199572 tlen-paired, 2834 hash-paired, 470 singletons, 13441 discordant, 383920 orphans, 10024 too large [>5000 bp], 11209395 duplicates)
Reads: 74615263 total, 41568 skipped (flags/unmapped)
Fragments: 37473155 total (37071844 tlen-paired, 1789 hash-paired, 503 singletons, 8895 discordant, 390124 orphans, 9006 too large [>5000 bp], 11549239 duplicates)
Reads: 81781006 total, 48314 skipped (flags/unmapped)
Fragments: 41076736 total (40596545 tlen-paired, 2801 hash-paired, 442 singletons, 13742 discordant, 463206 orphans, 21434 too large [>5000 bp], 12968388 duplicates)
Reads: 83236829 total, 78844 skipped (flags/unmapped)
Fragments: 41979072 total (40722075 tlen-paired, 3408 hash-paired, 485 singletons, 245958 discordant, 1007146 orphans, 103736 too large [>5000 bp], 13241737 duplicates)