# MappingQualityZeroBySample

Count of reads with mapping quality zero for each sample

## Overview

This annotation gives you the count of all reads that have MAPQ = 0 for each sample. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.

### Related annotations

• MappingQualityZero gives the count of reads with MAPQ=0 across all samples.
• LowMQ gives the proportion of reads with low mapping quality (MAPQ below 10, including 0).