I have single end data (Ion Torrent) and de novo assembly performed with MIRA (660 contigs) and SPADES (753 contigs). I just blasted few contigs it showed very less query coverage (17% of 63000 bp) and comparatively less identity (81%). Also performed reference assembly. Only 3% of the total reads aligned to the reference genome.
1. Why query coverage is very less?
2.Why less identity?
Thanks and Regards