# ChromosomeCounts

Counts and frequency of alleles in called genotypes

## Overview

This annotation outputs the following:

• Number of times each ALT allele is represented, in the same order as listed (AC)
• Frequency of each ALT allele, in the same order as listed (AF)
• Total number of alleles in called genotypes (AN)

### Example

AC=1;AF=0.500;AN=2

This set of annotations, relating to a heterozygous call(0/1) means there is 1 alternate allele in the genotype. The corresponding allele frequency is 0.5 because there is 1 alternate allele and 1 reference allele in the genotype. The total number of alleles in the genotype should be equivalent to the ploidy of the sample.