mcanouil
commented
2 years ago | Column Header | Description | Format | Examples | |
|---|---|---|---|---|
| SNPID | SNP/INDEL ID label from the imputation server, or from directly genotyped data | Text | 4:10229 / rs693 | |
| STRAND | Orientation of the site to the human genome strand used | + (Should be aligned to the forward strand) | + | |
| BUILD | Build of the genome on which the SNP is orientated | Numeric | 37 | |
| CHR | Chromosome on which the SNP resides | Numeric | 1 | |
| POS | Position of SNP on | Base pairs on human genome build used | 34000345 | |
| EFFECT_ALLELE | Allele for which the effect (BETA) is reported | SNP: Capital letter (A,C,G,T) / INDEL: Allele output by imputation server | A | |
| NON_EFFECT_ALLELE | Other allele at this site | SNP: Capital letter (A,C,G,T) / INDEL: Allele output by imputation server | G | |
| N | Total number of samples analysed at this site | Numeric, integer | 1234 | |
| N0 | Number of homozygous samples with zero copies of the EFFECT_ALLELE | Numeric, integer or float with 4 digits to the right of the decimal (imputed) | 623 / 745.2345 | |
| N1 | Number of heterozygous samples with one copy of the EFFECT_ALLELE | Numeric, integer or float with 4 digits to the right of the decimal (imputed) | 623 / 745.2345 | |
| N2 | Number of homozygous samples with two copies of the EFFECT_ALLELE | Numeric, integer or float with 4 digits to the right of the decimal (imputed) | 623 / 745.2345 | |
| EAF | Allele frequency of the EFFECT_ALLELE | Frequency with 4 digits to the right of the decimal | 0.3546 | |
| HWE_P | Exact HWE p-value for samples analysed, only if genotyped data is used in analysis | Scientific E notation with 4 digits to the right of the decimal (set to missing for imputed | SNPs) | 1.122E-02 / . |
| CALL_RATE | Genotyping call rate for the SNP (N_successful/N_attempted) | Frequency 4 digits to the right of the decimal. Set to 1.000 if imputed | 0.9936 | |
| BETA | Estimate of the effect size | Numeric float with 4 digits to the right of the decimal | 0.2036 | |
| SE | Estimated standard error on the estimate of the effect size, uncorrected for genomic control | Numeric float with 4 digits to the right of the decimal | 0.5611 | |
| PVAL | P value of the variant association | Scientific E notation with 4 digits to the right of the decimal | 3.244E-10 | |
| IMPUTED | Is the SNP/INDEL imputed? | 0 = Genotyped / 1 = Imputed | 1 | |
| INFO_TYPE | Type of information provided in the INFO column | Text, (set to missing if genotyped) | impute_info | |
| INFO | Measure of information content for the imputed SNP result | Numeric float with 4 digits to the right of the decimal (set to missing if genotyped) | 0.4832 / . |
burrowsk