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.
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".
UMI
- Mapped read pairs The number of mapped read pairs including specific, non-specific and broken read pairs before UMI grouping.
- 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".
- Proper UMI read pairs UMI read pairs that are mapped as pairs. The percentage is calculated relative to "UMI read pairs".
- Broken UMI read pairs UMI 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 "UMI read pairs".
- Specific proper UMI read pairs UMI read pairs that are mapped as pairs and are specific. The percentage is calculated relative to "UMI read pairs".
- Non-specific proper UMI read pairs UMI read pairs that are mapped as pairs, but are non-specific. 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.
The plot Reads by group size shows the number of proper input read pairs distributed by the size of the UMI groups that they have been grouped to. When running duplex UMI analyses, input read pairs that are grouped to duplex UMI read pairs are not represented in this plot.
The plot Groups by group size shows the number of UMI groups distributed by the UMI group sizes. When running duplex UMI analyses, duplex groups are not represented in this plot.
The plot Reads by group size (duplex) shows the number of proper input read pairs distributed by the size of the duplex UMI groups that they have been grouped to. If reads are not assigned to a duplex UMI group, they are not represented in this plot.
The plot Groups by group size (duplex) shows the number of duplex UMI groups distributed by the duplex UMI group sizes.
Realignment
- Realigned regions The number of regions that were subjected to local realignment, e.g. regions with long unaligned ends.
- Combined length of realigned regions The combined length of the locally realigned regions.
- Reassembled regions The number of regions that were subjected to reassembly, e.g. regions with significant unaligned end breakpoints.
- Combined length of reassembled regions The combined length of the reassembled regions.
Primer trimming
- Mapped read pairs The number of mapped read pairs including specific, non-specific and broken read pairs before UMI grouping.
- Discard read pairs without primer An option used when trimming for primer sequence, can be Yes or No.
- Read pairs without primers Read pairs that could not be assigned to a primer. If "Discard read pairs without primer" is set to yes, these reads will be discarded.
- Primer not found Read pairs not overlapping a primer.
- Inside alignment Read pairs overlapping a primer, but the primer is inside the alignment, not at the end.
- Not enough overlap Read pairs overlapping a primer, but the overlap is less than required as defined in the wizard step "Minimum primer overlap (%)".
- Read too short Read pairs where the remaining sequence of read 1 or read 2 is shorter than the threshold defined in the wizard step "Minimum read length after primer trim".
- Too many read mismatches Read pairs with at least 2 mismatches between the overlapping parts of the read and the primer.
- No primers on chromosome Read pairs mapped to chromosomes where there are no primers.
- Read pairs after primer trimming Read pairs remaining after primer trimming.
- Proper read pairs after primer trimming Read pairs that are mapped as pairs. The percentage is calculated relative to "Read pairs after primer trimming".
- Broken read pairs after primer trimming 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 primer trimming".
- Specific proper read pairs after primer trimming Read pairs that are mapped as pairs and are specific. The percentage is calculated relative to "Read pairs after primer trimming".
- Non-specific proper read pairs after primer trimming Read pairs that are mapped as pairs, but are non-specific. The percentage is calculated relative to "Read pairs after primer trimming".
Variant detection
- Ignored bases due to complex regions The number of bases where it was not possible to detect variants due to high complexity of the region.
- Ignored intervals due to complex regions The number of intervals where it was not possible to detect variants due to high complexity of the region.