Indexed Library Pools

Duplicate Filter Changes the Count Used for Coverage

Coverage uses duplicate-filtered unique reads, not raw reads. Exact arithmetic here means exact results for the stated model inputs; measured inputs still carry uncertainty and significant-figure limits.

highlighted = computed this step

Raw reads are not the coverage source

The raw read count is 30, with 6 duplicate reads.

raw=30,duplicates=6raw=30,\quad duplicates=6
Duplicate filter ledgerRaw read count minus duplicate read count pins the unique-read count.raw=30duplicates=6unique=24accepted=1

Coverage uses the duplicate-filtered count

The checked unique count is 24. This is the count later cited by coverage.

30  −  6=2430\;-\;6=24
Duplicate filter ledgerRaw read count minus duplicate read count pins the unique-read count.raw=30duplicates=6unique=24accepted=1