Mendelian Anomaly Detector
Spot embryonic lethality, sex-linked transmission, and CRISPR mosaicism the moment a litter genotypes out of expectation. Statistical, not vibe-based.
Available on the Pro plan ($99/mo)
⚠ Possible embryonic lethality
KO1/KO1 observed 0/12, expected 3.0. p = 0.042 · BF = 8.2
χ²
6.84
Goodness of fit
Bayes factor
Default threshold
FDR correction
Compares observed vs. Mendelian-expected
For every litter with genotyped pups, the detector computes the expected genotype distribution from parent genotypes using Mendelian rules, then runs a goodness-of-fit test against what was actually observed.
- χ² goodness-of-fit test for each litter and each genotype-bin combination
- Bayesian posterior probability of non-Mendelian transmission, with Bayes factor
- Aggregates across litters from the same pair to detect systemic effects
- Handles missing genotype data without dropping the litter from analysis
- Surfaces effect size alongside significance, so small samples do not over-flag
Punnett · Cre/+ × Cre/+
ExpectedObserved across last 5 litters
25%
50%
25%
Flags four common biology patterns
The detector classifies anomalies into interpretable categories so you know what to investigate. Pattern detection runs over all your litters by default and highlights the highest-confidence flags.
- Embryonic lethality: a homozygous class is missing or under-represented across multiple litters
- Sex-linked transmission: genotype-by-sex contingency table reveals X- or Y-linked inheritance
- CRISPR mosaicism: founder pair produces variable offspring genotypes inconsistent with single allele
- Genetic linkage: two-locus offspring distribution deviates from independent assortment
- Skewed sex ratio: ratio at birth deviates significantly from 1:1 across multiple litters
- Each pattern has an associated user-facing explanation and suggested next experiment
Embryonic lethality
criticalp = 0.012
Sex-linked
warningp = 0.034
CRISPR mosaicism
infop = 0.051
Genetic linkage
warningp = 0.029
Surfaces inside breeding and litter views
Anomaly badges appear directly on the litter list, the breeding pair page, and the strain dashboard. No separate Intelligence inbox to remember to check.
- Inline badge on the litter row with severity color (info, warning, critical)
- Pair-level rollup on the breeding page when multiple litters share the same anomaly
- Strain-level rollup when an anomaly appears across pairs of the same strain
- Click any badge to see the full math, the contributing litters, and a suggested action
- Optional weekly digest email summarizing flagged litters across the colony
Litter Records · 5 active
| Litter | Pair | Pups | Status |
|---|---|---|---|
| L-040 | B-19 | 8 (4M/4F) | expected |
| L-041 | B-23 | 6 (3M/3F) | expected |
| L-044 | B-32 | 12 (8M/4F) | lethality |
| L-045 | B-44 | 9 (1M/8F) | sex-skew |
| L-046 | B-19 | 7 (3M/4F) | expected |
Auditable math
Every flag is reproducible. The detector exports its inputs, expected distribution, observed distribution, test statistic, and p-value. Useful for IACUC audits and publication methods sections.
- One-click export of the full computation trace as JSON or PDF
- Methods page documents the exact statistical procedures used
- Configurable significance threshold per organization (default α = 0.05)
- Optional multiple-comparisons correction (Benjamini-Hochberg) for high-throughput colonies
- Reproducibility hash on every flag so two runs of the same data agree
{
"litterId": "L-2026-044",
"strainId": "JO_CatSperD",
"pair": { "male": "M-187", "female": "F-204" },
"test": "chi_square_goodness_of_fit",
"observed": { "Cre/Cre": 6, "Cre/+": 6, "+/+": 0 },
"expected": { "Cre/Cre": 3, "Cre/+": 6, "+/+": 3 },
"statistic": 6.84,
"df": 2,
"p_value": 0.042,
"bayes_factor": 8.2,
"interpretation": "embryonic_lethality",
"alpha": 0.05,
"fdr": "benjamini_hochberg",
"reproducibility_hash": "9f2a…b14e"
}Bring statistical rigor to your genetics
Anomaly detection is part of every Pro plan. No upgrade tier, no per-flag fee.