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Genome assembly, de-novo, less query coverage

Dear Sir/Madam,

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

next-gen assembly blast
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updated by Ram Ram • written by chullijoby • chullijoby

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