Count of reads with mapping quality zero for each sample
FORMAT (sample genotype-level)
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.
- 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).
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GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51.