# LowMQ

## Overview

This annotation tells you what fraction of reads have a mapping quality of less than the given threshold of 10 (including 0). Note that certain tools may impose a different minimum mapping quality threshold. For example, HaplotypeCaller excludes reads with MAPQ<20.

### Calculation

$$LowMQ = \frac{# reads with MAPQ=0 + # reads with MAPQ<10}{total # reads}$$