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Difference between mapping quality and minimum base quality

Hi all,

I am using Freebayes for haploid variant detection and I do not get the difference between parameters -m (mapping quality) and -q (minimum base quality). Could you help me, please?

Many thanks for your much appreciated help!

freebayes
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written by A_heath • A_heath

1 answer

Mapping quality (MAPQ) refers to probability that the mapping position is wrong. Base quality refers the score given to each nucleotide by the sequencing platform, and is an estimated probability of the base being incorrect. MAPQ takes base quality into account.

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written by dthorbur dthorbur

Thank you for your reply dthorbur!

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written by A_heath • A_heath

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