> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/genotype-cluster-plots-format.md).

# Genotype cluster plots format

The genotype cluster plot data files contain genotype intensities per variant for a subset of samples.

The subset of samples is selected so that from each separate genotyping batch a maximum of 100 samples is chosen from each call category (AA/homozygous ref; Aa/heterozygous; aa/homozygous alt).

Genotypes with a missing call are all selected. The columns of the data file are explained below.

| **Column**     | **Description**                                           |
| -------------- | --------------------------------------------------------- |
| ID             | Sample ID                                                 |
| batch          | Genotyping batch                                          |
| sex            | Sample sex                                                |
| intensity\_ref | Reference allele intensity                                |
| intensity\_alt | Alternative allele intensity                              |
| raw\_call      | Genotype call from chip                                   |
| imputed\_call  | Genotype call after imputation                            |
| excluded       | Whether sample was excluded from imputation (1=yes, 0=no) |

Read more about [cluster plots](/working-in-the-sandbox/working-with-genotype-data/cluster-plots.md).