Hi, It would be great, if anyone can help me to understand how bwa-mem alignment works when there is a pseudogene. When there is a region of gene which is 100% similar to the pseudogene and the generated reads are with a variant, then how the aligner will be able to map the reads to the correct location. Ideally I expected all the reads with mapping quality zero but I can see lots of reads with MAQ nearly 27 with the variant are mapped to gene and the reads with lower mapping quality without variant mapped to pseudogene. I am not getting how BWA is clearly placing the reads irrespective of the presence of repeat region. I have the attached the MSA which include the region of gene, psudogene and read with variant.
Thanks in advance.