Quality Control Report

Number of reads troughout th quality control process

Step	Output
raw	the input reads
deduplicated	after (optional) deduplication step
filtered	trimmed, quality filtered
qc	final reads, contaminants removed

Total number of reads/bases ater the QC

Quality values along the read

Read length

Insert size

The size of the reads + the space between. Ideally the paired-end reads don't overlap.