Deduplication
- Mapped read pairs The number of mapped read pairs including specific, non-specific and broken read pairs before deduplication.
- Duplicate read pairs Read pairs considered PCR duplicates.
- Read pairs after deduplication The number of mapped read pairs including specific, non-specific and broken read pairs.
- Proper read pairs after deduplication Read pairs that are mapped as pairs. The percentage is calculated relative to "Read pairs after deduplication".
- Broken read pairs after deduplication Mapped read pairs where the distance between the individual reads in the pair exceeded the expected distance for paired reads, or where only one of the reads in the pair was mapped. The percentage is calculated relative to "Read pairs after deduplication".
- Specific proper read pairs after deduplication Read pairs that are mapped as pairs and are specific. The percentage is calculated relative to "Read pairs after deduplication".
- Non-specific proper read pairs after deduplication Read pairs that are mapped as pairs, but are non-specific. The percentage is calculated relative to "Read pairs after deduplication".