GATK Non-model organism variant call SNP site all MQ same value

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Bekah W

• November 13, 2021 14:02

Why do I see all MQ as 60 in my variant SNP VCF file?

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  Pamela Bretscher

  • November 15, 2021 14:28

  Hi Bekah W,

  When the mapping qualities are very good at a particular site, it is expected for the MQ value to be around 60. This article explains a little bit more about what is expected for the MQ value. It seems that this is likely an indication that your reads are very high quality, but if you are still concerned or unsure, could you provide some more information about what you are seeing?

  Kind regards,

  Pamela 

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