> ## Documentation Index
> Fetch the complete documentation index at: https://primerlab-genomic.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

# Genotyping / Allele Discrimination

> Feature documentation: Genotyping / Allele Discrimination

Score primers for SNP genotyping assays (allele-specific PCR).

## Overview

The genotyping module evaluates primer suitability for allele-specific PCR:

* **SNP Position** - 3' terminal = best discrimination
* **Mismatch Type** - Transversions discriminate better than transitions
* **Tm Difference** - Higher delta Tm = better specificity

## Python API

### score\_genotyping\_primer\_api

```python theme={null}
from primerlab.api import score_genotyping_primer_api

result = score_genotyping_primer_api(
    primer_sequence="ATGCGATCGATCGATCGA",
    snp_position=0,        # Distance from 3' end
    ref_allele="A",
    alt_allele="T",
)

print(f"Grade: {result['grade']}")
print(f"Delta Tm: {result['delta_tm']}°C")
print(f"Specificity: {result['specificity']}")
```

## SNP Position Guidelines

| Position from 3' | Weight | Discrimination |
| ---------------- | ------ | -------------- |
| 0 (terminal)     | 1.0    | Best           |
| 1                | 0.7    | Good           |
| 2                | 0.4    | Acceptable     |
| 3                | 0.2    | Marginal       |
| 4+               | \<0.2  | Poor           |

## Mismatch Type Scoring

Transversions (purine ↔ pyrimidine) provide better discrimination:

| Mismatch | Score | Type                |
| -------- | ----- | ------------------- |
| A↔T      | 1.0   | Transversion (best) |
| G↔T      | 0.95  | Transversion        |
| A↔C      | 0.9   | Transversion        |
| G↔C      | 0.85  | Transversion        |
| A↔G      | 0.6   | Transition          |
| C↔T      | 0.6   | Transition          |

## Tm Discrimination

| Delta Tm | Specificity | Score |
| -------- | ----------- | ----- |
| ≥8°C     | Excellent   | 100   |
| ≥5°C     | Good        | 85    |
| ≥3°C     | Moderate    | 70    |
| ≥1.5°C   | Marginal    | 55    |
| \<1.5°C  | Poor        | 40    |

## Use Cases

1. **SNP Genotyping** - Detect known variants
2. **Mutation Screening** - Quick PCR-based detection
3. **Allele-Specific PCR (AS-PCR)** - Distinguish alleles

## See Also

* [Species Specificity](species-specificity)
* [Probe Binding](probe-binding)