# GWAS results format

The GWAS analysis produces the following types of files:

### Summary statistics

The summary statistics are bgzipped, [tabix-indexed](http://www.htslib.org/doc/tabix.html) tab separated files (.tsv). They contain the summary statistics of the [GWAS analysis](https://docs.finngen.fi/background-reading/gwas-analysis). The columns are:

| **Column**        | **Description**                           |
| ----------------- | ----------------------------------------- |
| #chrom            | chromosome                                |
| pos               | chromosomal position (in base pairs)      |
| ref               | reference allele                          |
| alt               | alternate allele                          |
| rsids             | rsIDs related to this variant             |
| nearest\_genes    | nearest genes                             |
| pval              | analysis p-value                          |
| mlogp             | -log10(p-value)                           |
| beta              | effect size of alternate allele           |
| sebeta            | standard error of effect size             |
| af\_alt           | allele frequency for the alternate allele |
| af\_alt\_cases    | alternate allele frequency in cases       |
| af\_alt\_controls | alternate allele frequency in controls    |

### Variant inclusion and INFO score

The GWAS analysis is performed for all variants in the genotype data, and the summary statistics contain all of these variants. These results are then uploaded to the green library, and shown in [pheweb](https://docs.finngen.fi/working-outside-the-sandbox/link-to-how-to-use-pheweb). An exception to this are variants with minor allele count less than 10, which are skipped during the GWAS analysis. For some subsequent analysis such as [fine-mapping](https://docs.finngen.fi/background-reading/finemapping), variants with INFO score lower than 0.6 are filtered out. For each release you can find the variant's INFO score, as well as other annotations, in the variant annotation file, which can be found in the green library. The path is: `gs://finngen-production-library-green/finngen_R[RELEASE_NUMBER]/finngen_R[RELEASE_NUMBER]_analysis_data/annotations/`

### Plots

The plots produced include three types of plots: [a manhattan plot](https://docs.finngen.fi/faq/about-pheweb/what-are-qq-and-manhattan-plots) of the GWAS, a manhattan plot with a log^2-scaled y-axis, and a [qqplot ](https://docs.finngen.fi/faq/about-pheweb/what-are-qq-and-manhattan-plots)of the GWAS.

Read more about[ GWAS analysis](https://docs.finngen.fi/background-reading/gwas-analysis). See more information about [What are QQ and Manhattan plots](https://docs.finngen.fi/faq/about-pheweb/what-are-qq-and-manhattan-plots).