When you are comparing a genome of two different isolates by using a high quality sequence or genome as a reference to identify differences, this is known as _____________ analysis

• A. Kmer based analysis
• B. PCA analysis
• C. wgMLST analysis
• D. hqSNP analysis

Answer: (D)

High-quality SNP (hqSNP) analysis. This approach maps sequencing reads from one genome to a high-quality reference genome and calls single-nucleotide differences at reliable positions, applying strict quality filters to keep only true SNPs. By focusing on these high-confidence nucleotide changes, you get fine-scale resolution of how the two isolates differ, which is ideal for inferring relatedness and constructing phylogenies.

Kmer-based analysis looks at shared short sequences without relying on a single reference alignment. PCA analysis is a statistical method for reducing data dimensions and clustering, not specifically about identifying differences between genomes. wgMLST analyzes allele differences across many genes rather than individual SNPs. The process described—using a high-quality reference to identify differences at the single-nucleotide level with stringent quality control—fits hqSNP analysis best.