Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (CO1), using ensembles of short-reads aligned to genetic barcodes that serve as digital proxies of the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. This subset of the full FASTQ file contains 4839 fragments, each between 100 and 200 nucleotides long, and their associated quality scores. These sequences were used in a novel method for assigning uncertainty to the NGS method employed.