[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
Loaded 735874 sites across 3366 contigs
Loaded 735874 sites across 3366 contigs
Reads: 4797 total, 663 skipped (flags/unmapped), 4134 no site overlap
Fragments: 0 total (0 paired, 0 singletons, 0 discordant, 0 orphans)
Sites: 735874 total, 0 with data, 0 output (depth>=10)
Reads: 1927049 total, 991 skipped (flags/unmapped), 255051 no site overlap
Fragments: 862358 total (808649 paired, 15 singletons, 0 discordant, 53694 orphans)
Sites: 735874 total, 174387 with data, 55783 output (depth>=10)