Count of all reads with MAPQ = 0 across all samples
This anotation gives you the count of all reads that have MAPQ = 0 across all samples. 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.
- MappingQualityZeroBySample gives the count of reads with MAPQ=0 for each individual sample.
- LowMQ gives the proportion of reads with low mapping quality (MAPQ below 10, including 0).
Return to top
Guide Index |
Tool Documentation Index |
GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51.