# Variant annotation file format

The variant annotation file contains annotations about the variants. Information such as batch-specific and across-batches INFO scores, allele counts, allele numbers, allele frequencies etc.

The column types are listed here:

| Column name            | Description                                                                                                                                                                                                                                                                                                              |
| ---------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| #variant               | variant id, formatted as CHROM:POS:REF:ALT                                                                                                                                                                                                                                                                               |
| chr                    | variant chromosome                                                                                                                                                                                                                                                                                                       |
| pos                    | position                                                                                                                                                                                                                                                                                                                 |
| ref                    | reference allele                                                                                                                                                                                                                                                                                                         |
| alt                    | alternate allele                                                                                                                                                                                                                                                                                                         |
| AC                     | allele count                                                                                                                                                                                                                                                                                                             |
| AC\_Het                | Heterozygote allele count                                                                                                                                                                                                                                                                                                |
| AC\_Het\_\*            | Batch-specific heterozygote allele count                                                                                                                                                                                                                                                                                 |
| AC\_Hom                | Homozygote allele count                                                                                                                                                                                                                                                                                                  |
| AC\_Hom\_\*            | Batch-specific homozygote allele count                                                                                                                                                                                                                                                                                   |
| AF                     | allele frequency                                                                                                                                                                                                                                                                                                         |
| AF\_\*                 | Batch-specific allele frequency                                                                                                                                                                                                                                                                                          |
| AN                     | Allele number                                                                                                                                                                                                                                                                                                            |
| CHIP\_\*               | Batch-specific Chip genotyped variant marker                                                                                                                                                                                                                                                                             |
| HWE\_\*                | Batch-specific Hardy-Weinberg test                                                                                                                                                                                                                                                                                       |
| INFO                   | imputation INFO score                                                                                                                                                                                                                                                                                                    |
| INFO\_\*               | Batch-specific imputation INFO score                                                                                                                                                                                                                                                                                     |
| NS                     | Number of samples with data                                                                                                                                                                                                                                                                                              |
| NS\_\*                 | Batch-specific number of samples with data                                                                                                                                                                                                                                                                               |
| gene\_most\_severe     | gene affected by the most severe consequence                                                                                                                                                                                                                                                                             |
| most\_severe           | most severe consequence as predicted by VEP                                                                                                                                                                                                                                                                              |
| rsid                   | rsid(s) of the variant                                                                                                                                                                                                                                                                                                   |
| b37\_coord             | Build 37 (hg19) coordinates for variant                                                                                                                                                                                                                                                                                  |
| EXOME\_enrichment\_\*  | variant enrichment in Finnish population against multiple non-Finnish populations (non-Finnish Europeans (nfe), non-Finnish, Non-Swedish Europeans, (nfse), non-Finnish,non-Estonian Europeans (nfee), non-Finnish, non-Swedish, non-Estonian Europeans (nfsee) ) . Allele frequencies taken from gnomAD 2.1 exome data. |
| EXOME\_AF\_\*          | Allele frequencies for different populations, from gnomAD 2.1 exome data.                                                                                                                                                                                                                                                |
| GENOME\_enrichment\_\* | variant enrichment in Finnish population against multiple non-Finnish populations (non-Finnish Europeans (nfe), non-Finnish,non-Estonian Europeans (nfee)) . Allele frequencies taken from gnomAD 2.1 exome data.                                                                                                        |
| GENOME\_AF\_\*         | Allele frequencies for different populations, from gnomAD 2.1 genome data.                                                                                                                                                                                                                                               |


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