Compute how many backcross generations and how many months it takes to reach a target recipient genome proportion — with or without marker-assisted speed congenic.
Try it out
Load example backcross-to-congenic calculator data to see the full workflow
Fraction of the genome that should match the recipient strain (0.51 – 0.9999).
Default 0.5 (F1 from donor × recipient). Override if you are continuing an in-progress backcross.
Mating to next mating. Default 11 weeks for B6-class strains.
| Generation | Conventional | Speed (MAS) | Weeks |
|---|---|---|---|
| N1 | 75.00% | 87.50% | 11 |
| N2 | 87.50% | 96.88% | 22 |
| N3 | 93.75% | 99.22% | 33 |
| N4 | 96.88% | 99.80% | 44 |
| N5 | 98.44% | 99.95% | 55 |
| N6 | 99.22% | 99.99% | 66 |
| N7 | 99.61% | 100.00% | 77 |
| N8 | 99.80% | 100.00% | 88 |
| N9 | 99.90% | 100.00% | 99 |
| N10 | 99.95% | 100.00% | 110 |
| N11 | 99.98% | 100.00% | 121 |
| N12 | 99.99% | 100.00% | 132 |
Green cells indicate the first generation to reach your target proportion on each path.
When to use
Do not use for
Backcrossing converges on recipient *outside* the target locus. The 1-2 cM around your gene of interest stays donor — that's the linkage drag. Speed congenic shrinks this drag faster than conventional.
Some labs call F1 "N1," others call it "F1" and the first backcross "N1." Always say "X backcrosses to recipient" and quote the percentage. This calculator uses backcross count.
A mouse generation is 10-12 weeks if everything goes right. Half your delay comes from rebreeding old males, occasional mis-genotyping, and the dam that doesn't plug. Always pad your timeline by 25%.
If your target phenotype is robust (e.g., a survival assay), conventional backcrossing is fine. If it's a behavioral or immunological readout where background noise dominates, speed congenic is worth the SNP cost.
Conventional: recipient(N) = 1 − (1 − starting) (0.5)^N. Default starting = 0.5 (F1). Speed congenic with marker-assisted selection: recipient(N) = 1 − (1 − starting) (0.25)^N (Markel et al. 1997). Generation time defaults to 11 weeks per backcross (mating to next mating). Search returns the smallest N reaching the target. Per-generation table runs N1-N12 for both paths.
Last validated 2026-04-06. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.
ConductScience Backcross-to-Congenic Calculator (v1.0.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/backcross-congenic-calculator
Markel P, Shu P, Ebeling C, Klingenstein G, Sansone J, Klein J, et al. Theoretical and empirical issues for marker-assisted breeding of congenic mouse strains. Nat Genet. 1997;17:280-284.
Wakeland E, Morel L, Achey K, Yui M, Longmate J. Speed congenics: a classic technique in the fast lane (relatively speaking). Immunol Today. 1997;18:472-477.
Move a single gene, transgene, or chromosomal region from a donor strain onto a recipient strain background, *without* dragging along thousands of donor SNPs that could confound your phenotype.
1. Cross donor recipient → F1 (50% recipient genome, all heterozygous at the target locus) 2. Backcross F1 carrier recipient → BC1 (75% recipient on average) 3. Genotype the offspring, pick carriers, repeat 4. After ~10 backcrosses, the donor genome outside the target locus is <0.1% 5. Intercross two carriers to get a homozygous congenic stock
recipient proportion = 1 − (donor at start) (0.5)^N. With F1 starting at 50% recipient, donor halves every generation. Geometric, not linear.
A "knock-out on a 129 background" is a different mouse than the same knock-out on a B6 background. Behavioral, immunological, and metabolic phenotypes can flip sign on a different background. If you want your paper to replicate, your KO needs to be on the background everyone else uses — usually B6.
Conventional backcrossing wastes time because you pick carriers blind. Even after 5 generations, the carrier you bred from might happen to have an unlucky 35% donor background — pulling the average back up.
Genotype 96-384 SNP markers spaced across the genome on every potential breeder. Pick the carrier whose *background* is most recipient — the one that "won" the random shuffle that generation. Markel et al. (1997) showed this gets you N10-equivalent in 4-5 generations instead of 10.
If your target locus is on a chromosome with already-low recipient density, MAS gains less. If the line is a permanent backbone strain (not a one-shot project), the time savings dominate.
Logs each backcross generation, rolls up genotype calls automatically, and projects the date your line hits the congenic threshold.
Open app EquipmentPlan the breeding cohort for each backcross generation — how many trios, dams, and cages to deliver enough carriers.
Browse QuoteGet a quote on equipment or talk to the ConductScience team.
Request quote