Index of Autoreporting variables

The group reports contain the group-level summary of a autoreporting run. It is a .tsv file with one row per one group. The columns are as follows:

The group reports contain

Column	Description	Example value/Formatting
phenotype	phenotype name	-
phenotype_abbreviation	phenotype code	-
Cases	Number of cases for this phenotype	1234
Controls	Number of controls for this phenotype	1234
locus_id	The locus in question, formatted from the top SNP's chromosome, position, reference and alternate alleles. In case of credible set grouping, the top SNP is the variant with the largest PIP in that credible set. In case of LD and simple grouping, the top SNP is the variant with smallest p-value of that group/region. Most if not all release results are grouped around credible sets.	chr1_1_C_T for a lead variant with chromosome 1, position 1, reference allele C and alternate allele T.
chrom	chromosome of locus	1
pos	lead variant position	123456
ref	lead variant reference allele	A
alt	lead variant alternate allele	C
pval	lead variant p-value	5.01e-7
start	locus start position in basepairs	1 for a group with positions [1,2,3,4,5]
end	locus end position in basepairs	5 for a group with positions [1,2,3,4,5]
lead_enrichment	How much the lead variant is enriched in Finnish population compared to Europe	4.35
lead_$COLUMN_NAME	other columns that are grabbed for the lead variant, such as allele frequencies, effect size, variant RSIDs	-
most_severe_gene*	most severe gene of the lead variant	APOE
most_severe_consequence	most severe consequence of lead variant	missense_variant
gnomAD_functional_category	functional category for the variant Exome data.	pLoF
gnomAD_enrichment_nfsee	lead variant enrichment in Finland against NFSEE population. Exome data.	5.1
gnomAD_fin.AF	lead variant allele frequency in Finland. Exome data.	0.123
gnomAD_fin.AN	lead variant allele number in Finland. Exome data.	123
gnomAD_fin.AC	lead variant allele count in Finland. Exome data.	123
gnomAD_fin.homozygote_count	Amount of homozygote carriers in Finnish population. Exome data.	12
gnomAD_fet_nfsee.odds_ratio	Fischer's exact test for enrichment FIN vs NFSEE odds ratio. Exome data.	1.15
gnomAD_fet_nfsee.p_value	Fischer's exact test for enrichment FIN vs NFSEE p-value. Exome data.	5.01e-3
gnomAD_nfsee.AC	lead variant NFSEE population allele count. Exome data.	123
gnomAD_nfsee.AN	lead variant NFSEE population allele number. Exome data.	123
gnomAD_nfsee.AF	lead variant NFSEE population allele frequency. Exome data.	0.123
gnomAD_nfsee.homozygote_count	Amount of homozygote carriers in NFSEE population. Exome data.	123
cs_id	credible set id	chr1_123456_A_C_1
cs_size	credible set size	5
cs_log_bayes_factor	credible set bayes factor, log10	5.21
cs_number	credible set number in its region	1
cs_region	finemapping region	1:1-30000001
found_associations_strict	This column lists all of the trait associations found in GWAS Catalog for variants that are in the credible set/strict group (strict group here means that in case of LD grouping, variants that are in higher LD than a given threshold, and have p-values lower than the significance threshold). The trait name is followed by the amount of correlation (in R²) that association had with the lead variant. If there are multiple variants associated with that trait, the largest value is chosen.	`trait1\
found_associations_relaxed	This column lists all of the trait associations found in GWAS Catalog for variants in the group. The trait name is followed by the R² to lead value of the variant that had the association. If there are multiple variants associated with that trait, the largest value is chosen.	`trait1\
credible_set_variants	This column lists the credible set variants. The PIP and R² values are listed after the variant	`chr1_1_C_T\
functional_variants_strict	All of the variants with a functional consequence, with the functional consequence label and R² to lead variant. The variants are part of the credible set/strict group.	`chr1_1_C_T\
functional_variants_relaxed	All of the variants with a functional consequence, with the functional consequence label and R² to lead variant. The variants are part of the credible set/strict group.	`chr1_1_C_T\
specific_efo_trait_associations_strict	If specific traits were given to the script(e.g. equivalent EFO codes to the phenotype in question), any trait associations correspoding to those traits are listed here. This column lists only associations where the variant is in the credible set/strict group.	Same formatting as found_associations_strict
specific_efo_trait_associations_relaxed	If specific traits were given to the script(e.g. equivalent EFO codes to the phenotype in question), any trait associations correspoding to those traits are listed here. This column lists associations to all variants in the group.	Same formatting as found_associations_relaxed
credible_set_min_r2_value	The minimum R² value to lead variant in the credible set	0.489

*The HGNC symbols in the autoreporting files are version 38, as well as the VEP cache. "The most_severe_gene" and "most_severe" columns in the autoreporting file come from the finngen annotation file. Analysis team will update the release documentation to include this information (including those versions) for future releases.