Our system infers karyotype by calculating the ratio of deduplicated reads mapped to chromosome X (chrX) and chromosome Y (chrY). Based on pipeline-specific, empirically validated thresholds, we classify samples into one of the following categories:
- XX: Female
- XY: Male
- Other – This classification applies when the observed ratios of chrX and chrY reads do not fall within our defined thresholds, meaning we cannot make a high-confidence determination.
Additionally, if a sample has zero deduplicated mapped reads, it will result in an Unknown classification, as there is insufficient data to determine karyotype.
If you have any questions or need further clarification, please reach out to our support team.