Question: Difference between Alignment quality and Mapping quality
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gravatar for ammarsabir15
2.1 years ago by
ammarsabir1560
ammarsabir1560 wrote:

I want to ask is there any difference between alignment quality and mapping quality of BAM file ??

bam next-gen sequence • 1.3k views
ADD COMMENTlink modified 2.1 years ago by jh.monin20 • written 2.1 years ago by ammarsabir1560
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gravatar for jh.monin
2.1 years ago by
jh.monin20
jh.monin20 wrote:

Alignment score is the quality of of matching between the read-sequence and reference-sequence. Mapping quality is the confidence that the read is correctly mapped to the genomic coordinates. For example, a read may be mapped to several genomic locations with almost a perfect match in all locations. In that case, alignment score will be high but mapping quality will be low.

ADD COMMENTlink written 2.1 years ago by jh.monin20
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