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Proportion of low quality reads

Category Annotation Modules

VCF Field INFO (variant-level)

Header definition line
  • INFO=<ID=LowMQ,Number=3,Type=Float,Description="3-tuple: <fraction of reads with MQ=0>

  • 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.


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

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.