Something does not appear to be right (are you using the correct genome).
Are you using new version of *ALL* programs (samtools/bcftools) in this pipeline?
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Code:
531380 (0.86%) aligned exactly 1 time 16490453 (26.84%) aligned >1 times 27.70% overall alignment rate
BTW: Please create new threads for new questions. Your question is not related to the original thread.
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