Hi there! We sequenced some chicken genomic DNA (Illumina TruSeq, PE150), and I am trying to map the reads to reference genome with BWA mem and then call SNPs with GATK. I used the default settings of BWA, and checked the alignment statistics by using samtools flagstat. I got a 99% mapping rate. Does this mapping rate seem to be in normal range? I'm very new to DNA-seq alignment. It would be great if you guys could give me some suggestions about adjusting BWA parameters for PE150. Any input will be appreciated!