Hi, I am very new to NGS analysis. I want to do WES analysis on a normal human embryonic stem cell line. I have aligned the paired-end reads (2* 150) on the the hg38 with bowtie2 and bwamem. after the alignment and then realignment around the indel, I checked the quality with the qualimap2 and I got VERY different result for mismatches, insertion, and indels.
Mismatches and indels (inside of regions)
Bowtie2 results: General error rate 1.11% Mismatches 35,875,622 Insertions 6,729,119 Mapped reads with at least one insertion 6.51% Deletions 812,397 Mapped reads with at least one deletion1.26% Homopolymer indels 16.81%
BWAmem result: General error rate 0.27% Mismatches 20,648,892 Insertions 276,090 Mapped reads with at least one insertion 0.33% Deletions 332,003 Mapped reads with at least one deletion 0.4% Homopolymer indels 59.3%
My questions are: 1. This is a normal cell line (not cancerous)! Should I expect this many mismatches? 2. Should I expect such a difference between the bowtie2 and bwa mem results?