Estimate mutation rate per base pair per generation from observed mutations, generations, genome size and lineages.
Averages over lineages and generations: it assumes mutations accumulate linearly and are counted without selection bias. Mutation-accumulation designs (small bottlenecks, minimal selection) approximate this best.
Mutation rate (per bp per generation)
How to use this tool
The total number of verified mutations across all lineages.
The number of generations over which mutations accumulated.
The haploid genome size in base pairs (E. coli is about 4.6 million).
The number of independent lines or replicates contributing mutations.
Formula & worked example
30 mutations over 1000 generations, 4.6 million bp genome, 10 lineages: rate = 30 / (1000 × 4.6×10⁶ × 10) ≈ 6.522×10⁻¹⁰ per bp per generation, or 0.003 mutations per genome per generation.
Limitations — read this before you rely on it
Assumes neutral accumulation and complete detection. Selection removes deleterious mutations, sequencing misses some, and rates vary across the genome — the result is a genome-wide average.
Frequently asked questions
Roughly 10⁻¹⁰ to 10⁻⁹ per base per generation in bacteria, and around 10⁻⁸ per base per generation in humans (per diploid genome the numbers differ by ploidy).
Each lineage is an independent accumulation experiment. Pooling mutations without dividing by lineage count would inflate the rate.
Repeated single-cell bottlenecks minimise selection, so even mildly deleterious mutations survive to be counted — giving a truer spontaneous rate.
Per base compares organisms fairly; per genome shows the mutational load each offspring actually carries. Both are shown here.
Yes — hotspots, repeats, transcription-coupled repair and local sequence context all create variation around the genome-wide average.