Why would I only see mapping qualities less than or equal to 40 for all called variants? GenotypeGVCFs for 37 non-model organism individuals produces the same distribution of mapping qualities for all chromosomes where there is a continuous range of mapping qualities starting at MQ=20 until MQ=40 where it abruptly stops. However, there is an unusually high frequency of calls with exactly MQ=40.
This is my first try at SNP calling, and I am at a loss for an explanation for this pattern. The attached image is a histogram of MQ for all unfiltered called variants for one chromosome. The pattern is the exact same for all chromosomes.
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