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Table 4 Validated pathogen identifications in patients with neurological infections have high numbers of unique k-mers per read. The pathogens were identified with as few as 15 reads, but the high number of unique k-mers indicates distinct locations of the reads along their genomes. Re-alignment of mapped reads to their reference genomes (column “Covered bases”) corroborates the finding of the unique k-mers (see also Additional file 1: Figure S4). Interestingly, the k-mer count in PT5 indicates that there might be multiple strains present in the sample since the k-mers cover more than one genome. Read lengths were 150–250 bp

From: KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

Sample Matched microorganism Reads k-mers Covered bases
PT5 Human polyomavirus 2 9650 7129 5130/5130
PT7 Elizabethkingia genomo sp. 3 403 20,724 53,256/4,433,522
PT8 Mycobacterium tuberculosis 15 1570 2227/4,411,532
PT10 Human gammaherpesvirus 4 20 2084 2822/172,764