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BWA alignment

We sequenced some chicken genomic DNA (Illumina TruSeq, 150PE) for SNP calling. I did reads alignment with BWA mem, default settings, then checked the statistic by using flagstat. The mapping rate is >99%. I'm wondering is this mapping rate normal? If not, what's your suggestions to tune bwa parameters. Thank you very much!

Best Answers


  • TechnicalVaultTechnicalVault Cambridge, UKMember ✭✭✭

    BWA MEM is rather aggressive in mapping reads so what you should probably check is the properly paired reads %.

  • The percentage of properly paired reads is 92%.

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