This project investigates whether short-read sequencing of three evolved E.
coli Ara-3 lineages can identify the genetic basis of divergent mutation rates.
From raw FASTQ reads, a reproducible pipeline (QC, alignment, haploid calling, filtering, annotation) compares mutation burden across lineages.
It tests whether one lineage has become a hypermutator, shown by a large, largely unique variant burden co-occurring with mismatch-repair mutations (mutS, mutL), and whether lineages share adaptive pykF mutations reflecting convergent selection.