Genotype Quality

Genotype Quality in Genetics

Genotype quality (GQ) is a measure used in genetics to indicate the confidence of a genotype call at a specific genomic position. It represents the probability that the called genotype is incorrect, with higher values indicating greater confidence in the genotype assignment.

What is Genotype Quality?

When calling variants from sequencing data, genotype quality provides an estimate of how reliable the genotype assignment is at each variant site. It takes into account factors such as the number and quality of reads supporting each allele, the overall depth of coverage, and the expected allele frequencies in the population.

Genotype quality is typically represented as a Phred-scaled score, similar to mapping quality. A genotype quality of 20 indicates there is a 1 in 100 chance that the called genotype is incorrect, while a score of 30 means there is a 1 in 1000 chance of an incorrect genotype.

Examples

• A genotype quality of 10 means there is a 1 in 10 chance (10%) that the genotype call is incorrect. This is considered a low-confidence genotype call.
• A genotype quality of 50 indicates there is only a 1 in 100,000 chance (0.001%) that the genotype is incorrect. This represents a high-confidence genotype call.
• In a clinical setting, a genotype quality threshold of 20 or 30 might be used to filter out low-confidence genotype calls before reporting variants to patients.

Real-Life Interpretations

1. Rare Variant Analysis: When searching for rare disease-causing variants, setting a high genotype quality threshold (e.g., GQ > 30) can help prioritize high-confidence genotype calls and reduce false positives.
2. Genome-Wide Association Studies (GWAS): In GWAS, where large numbers of samples are genotyped, genotype quality can be used to filter out low-confidence genotypes that might introduce noise into the association analysis.
3. Mendelian Inconsistencies: In family-based studies, genotype quality can help identify Mendelian inconsistencies, where the genotypes of the offspring are incompatible with the genotypes of the parents. Low genotype quality at these sites might indicate genotyping errors.
4. Allele Frequency Estimation: When estimating allele frequencies in a population, genotype quality can be used to weight the contribution of each genotype, with higher-quality genotypes contributing more to the frequency estimate.

The interpretation of genotype quality can depend on the specific tools and algorithms used for variant calling. Some variant callers, like GATK, provide a more detailed breakdown of genotype quality that takes into account additional factors like strand bias and mapping quality.