Mapping statistics
- References The number of sequences in the reference genome.
- Input read pairs Total number of read pairs in the fastq files.
- Read pairs remaining after trimming The number of read pairs left after trimming.
- Unmapped read pairs The number of read pairs that could not be mapped to the reference.
- Mapped read pairs The number of mapped read pairs including specific, non-specific and broken read pairs.
- Mapped proper read pairs Read pairs that are mapped as pairs. The percentage is calculated relative to "Mapped read pairs".
- Mapped broken read pairs 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 "Mapped read pairs".
- Mapped specific proper read pairs Read pairs that are mapped as pairs and are specific. The percentage is calculated relative to "Mapped read pairs".
- Mapped non-specific proper read pairs Read pairs that are mapped as pairs, but are non-specific. The percentage is calculated relative to "Mapped read pairs".
Insert size distribution
Plot showing the distribution of insert sizes in specific proper read pairs. The insert is defined as the distance between the 5' ends of R1 and R2. If reads are quality trimmed from the 5' end or are trimmed for UMI and common sequence, the removed bases are not included when calculating the insert size.