Dear all, I have aligned my 300*2 data against a 4 Mb reference using both Bowtie2 and bwa-0.7.

The alignment percentage observed in bowtie2 is 80% and with bwa it is 99%. What is fundamentally different causing such a large difference between the aligners.

The coverage once calculated from the mpileup drops tp 1% at 20x. So, the depth is low in both the methods. But bwa has a better horizontal coverage in terms of alignment but depth drops in this too.

Thanks