Summary
Percentages in the summary table are calculated relative to Input read pairs, unless the value is preceded by a hyphen. In such cases, the percentage is calculated relative to the last non-hyphenated value listed above.
- Input read pairs Total number of read pairs in the fastq files.
- Read pairs discarded by quality trimming Trimmed read pairs, that after trimming are shorter than specified in the option "Minimum read length after quality trim" and have been discarded.
- Read pairs trimmed by quality trimming Read pairs that have been trimmed and are longer than "Minimum read length after quality trim".
- Read pairs discarded by adapter trimming Trimmed read pairs, that after trimming are shorter than specified in the option "Minimum read length after adapter trim" and have been discarded.
- Read pairs trimmed by adapter trimming Read pairs that have been trimmed and are longer than "Minimum read length after adapter trim".
- Average read length before trimming Average length of reads in input.
- Average read length after trimming Average length of reads after quality trimming and adapter trimming.
- Read pairs remaining after trimming Read pairs remaining after quality and adapter trimmming. These are the read pairs that are mapped.
- Unmapped read pairs Read pairs that did not map to the reference.
- Mapped read pairs The total number of mapped read pairs including specific, non-specific and broken pairs.
- Proper read pairs Read pairs that are mapped as pairs. The percentage is calculated relative to "Mapped read pairs".
- 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".
- Specific proper read pairs Read pairs that are mapped as pairs and are specific. The percentage is calculated relative to "Mapped read pairs".
- 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".
- Average insert size Average insert size calculated from specific proper read pairs.
- Median insert size Median insert size calculated from specific proper read pairs.
- Read pairs removed as duplicates Read pairs removed as duplicate read pairs.
- UMI read pairs Read pairs after UMI grouping.
- Singleton UMI read pairs UMI read pairs generated from only one read pair. The percentage is calculated relative to "UMI read pairs".
- Simplex UMI read pairs UMI read pairs where input reads all originate from the same strand. Singleton UMI read pairs are a subset of the simplex UMI read pairs. The percentage is calculated relative to "UMI read pairs"
- Duplex UMI read pairs UMI read pairs that are based on input reads from both strands. The percentage is calculated relative to "UMI read pairs"
- Average number of reads per UMI The average number of read pairs per UMI read pair.
- Median number of reads per UMI The median number of read pairs per UMI read pair.
- Average number of reads per duplex UMI The average number of read pairs per duplex UMI read pair.
- Median number of reads per duplex UMI The median number of read pairs per duplex UMI read pair.
- Read pairs discarded during primer trimming Read pairs discarded during primer trimming.
- Read pairs removed due to ligation artifacts The number of read pairs that were identified as ligation artifacts and removed from the mapping.
- Read pairs remaining for variant detection All read pairs remaining after processing, including both proper and broken read pairs, and specific and non-specific read pairs.