Query coverage is the % of sequence aligned to a sequence in the genebank. Low query coverages result from short sequences or, your sequence has a good size but sequences on GenBank are too short, or your sequence is too different from every sequence in Genbank. The smaller is the query coverage, the fewer nucleotides are been compared and the chance or error (E) is higher. So if the E value of the query is =0 it doesn't matter if the query coverage is