Statistics table for each mapping
By checking Create table with statistics for each mapping, a table showing detailed statistics for each reference sequence will be generated (figure 19.19).
Figure 19.9: Statistics table for a read mapping.
- Contig
- Reference name
- Reference Latin name
- Reference description
- Reference length
- Mapped reads
- Forward reads
- Reversed reads
- Reads in aligned pairs
- Reads in broken pairs: wrong distance or mate inverted
- Reads in broken pairs: mate on other contig
- Reads in broken pairs: mate not mapped
- Mean distance
- Standard deviation. Standard deviation of the mapped pairs distances.
- Non-specific matches
- Non-perfect matches
- Minimum coverage
- Maximum coverage
- Average coverage
- Standard deviation. Standard deviation of the per base coverage.
- Minimum excluding zero coverage regions
- Average excluding zero coverage regions
- Standard deviation excluding zero coverage regions. Standard deviation of the per base coverage, excluding regions without coverage.
- % GC. GC content of the reference sequence.
- Consensus length
- Fraction of reference covered
- Count (zero coverage regions)
- Minimum length (zero coverage regions)
- Maximum length (zero coverage regions)
- Average length (zero coverage regions)
- Standard deviation (zero coverage regions). Standard deviation of the distribution of the lengths of all the zero coverage regions on that contig.
- Total length (zero coverage regions)