SamTools

Percent mapped

Figure 1 : horizontal barplot representing mapping quality.

Source : nf-core RNAseq MultiQC

The y-axis represents the different samples and the x-axis represents the percentages of readings according to their mapping quality.

There are three main metrics :

• Mapped (with Mapping Quality (MQ)>0): This metric corresponds to the number of reads mapped with satisfactory alignment quality.
• MQ0: This metric represents the number of reads that could have been mapped, but whose alignment quality is too low (MQ=0).
• Unmapped: This metric corresponds to the number of unmapped reads.

A low alignment quality indicates an insufficient confidence probability for this read. Reads with an alignment quality of 0 can mean three different things:

The read is not part of the reference, which can be due to contamination or a little-known reference genome.

The reading is not part of the reference, which may be due to contamination or a non-complete genome. If the alignment quality is really very low, this may also be due to too high a level of multimapping.

Consequently, the majority of your reads should be mapped at around 90% for a well-known genome. In the case of a less well-known reference genome, or when using more distantly related species, this rate may drop to 70/80%.