When you are comparing a genome of two different isolates by comparing a gene-by-gene (locus-by-locus) basis to find differences, this is known as ________________ analysis

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

Answer: (A)

The idea here is comparing many gene loci across genomes to generate an allelic profile for each isolate. This approach is best described by whole-genome MLST, which extends traditional multilocus sequence typing to thousands of loci across the genome and assigns an allele number to each gene. By comparing these locus-by-locus allelic differences, you can assess relatedness between isolates with high resolution, including both core and accessory genes in the pan-genome.

This differs from other methods: k-mer based analysis compares genomes by shared short sequences without relying on predefined gene loci; PCA is a statistical visualization/analysis technique that can be applied to various data types but isn’t itself a gene-by-gene comparison method; high-quality SNP analysis focuses on single-nucleotide differences relative to a reference rather than allelic differences across many gene loci.