STAR

Alignment score

Figure 1 : bar charts representing the reads categorized by their alignment family.

source : nf-core RNAseq MultiQC

In Figure 1, each sample is shown on the ordinate and the percentage of readings on the abscissa.

Metrics :

Uniquely mapped : reads that are aligned to only one location in the reference genome.

Mapped to multiple loci : reads that are aligned to multiple locations in the reference genome while still being usable for data processing.

Mapped to too many loci : reads that are aligned too many times across the reference genome, resulting in a very low-quality score.

Unmapped too short : reads that are not aligned because they were too short.

Unmapped other : reads that are not aligned because they were not found in the reference genome or because they are of too low quality.

If there are too many multi-mapped sequences, it may be because the reads were too short or the tested genome has many duplications. The graph above shows a good result: we expect at least 90% of reads to be Uniquely mapped.