ATLAS quality control report

Total reads per sample

Step Output
raw The input reads specified in the configuration
deduplicated Counts after (optional) deduplication step
filtered Low quality reads have been removed
clean Contaminants removed
QC Passing reads -- for metagenomic samples, 16S reads are returned to sequence pool

Total bases per sample

For details see Table T1.

Reads quality before QC

Reads quality after QC

Paired end

Single end

Paired end reads that lost their mate during filtering.

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