Build Summary
Release Version: 20230706150541
New: We are pleased to present the NCBI ALFA Release 3 (version 20230706150541), one of the largest and most comprehensive aggregated variant databases that includes allele and genotype frequency. This version incorporates new genotype frequency and Hardy-Weinberg equilibrium(HWE) probability to help you analyze more effectively. All of these information are now in our FTP files.
##FORMAT=<ID=HWEP,Number=1,Type=Integer,Description="int(-log(HWE score test p-value)); -1 indicates that the HWE score test p-value could not be computed">
##FORMAT=<ID=GR,Number=1,Type=Integer,Description="Genotype homozygous reference allele (AA) count; in rare cases may not be the GRCh reference allele">
##FORMAT=<ID=GV,Number=1,Type=Integer,Description="Genotype heterozygous ref/alt (A/B) count; reported for the most common two alleles that may or may not include the reference allele">
##FORMAT=<ID=GA,Number=1,Type=Integer,Description="Genotype homozygous alternate allele (B/B) count; could be any of the non-biallelic variant alleles.">
The RefSNP website already reports the frequency of alleles from this release. We are planning to update the RefSNP page to include genotype frequency and Hardy-Weinberg equilibrium (HWE) probability.
Input and Output Counts
| Input | Count |
|---|---|
| Studies | 82 |
| Subjects | 204,108 |
| Genotypes | 5,773,169,974,362 |
| Output | Count |
|---|---|
| Total RefSNPs | 904,666,942 |
| Exist in dbSNP 156 | 904,113,309 |
| Novel | 553,633 |
* Subject counts for different assay source can be overlapping.
| Population | Biosample ID | Subjects | Total Site Count | MAF = 0 | MAF >= 0.01 | 0.01 > MAF >= 0.001 | MAF < 0.001 | Singleton |
|---|---|---|---|---|---|---|---|---|
| European | SAMN10492695 | 170,432 | 897,795,726 | 790,467,870 | 12,698,121 | 10,217,165 | 874,880,440 | 55,468,196 |
| AfricanOthers | SAMN10492696 | 330 | 889,789,877 | 867,263,040 | 16,189,977 | 6,336,860 | 867,263,040 | 6,693,257 |
| EastAsian | SAMN10492697 | 2,515 | 889,359,780 | 877,818,106 | 11,382,903 | 133,481 | 877,843,396 | 3,530,766 |
| AfricanAmerican | SAMN10492698 | 8,860 | 890,733,488 | 823,801,666 | 17,221,278 | 17,452,425 | 856,059,785 | 25,341,328 |
| LatinAmerican1 | SAMN10492699 | 817 | 889,296,648 | 869,911,354 | 12,614,612 | 6,770,380 | 869,911,656 | 6,683,777 |
| LatinAmerican2 | SAMN10492700 | 4,703 | 889,338,588 | 862,580,163 | 9,603,034 | 17,148,712 | 862,586,842 | 11,064,663 |
| OtherAsian | SAMN10492701 | 1,000 | 889,157,433 | 880,613,029 | 8,495,071 | 41,203 | 880,621,159 | 2,585,443 |
| SouthAsian | SAMN10492702 | 2,619 | 889,137,055 | 875,447,223 | 13,542,288 | 139,843 | 875,454,924 | 4,210,232 |
| Other | SAMN11605645 | 12,832 | 897,815,333 | 859,256,511 | 14,990,800 | 22,453,126 | 860,371,407 | 14,080,922 |
| African (note 1) | SAMN10492703 | 9,190 | 890,733,974 | 822,797,281 | 17,256,003 | 17,786,640 | 855,691,331 | 25,853,998 |
| Asian (note 2) | SAMN10492704 | 3,515 | 889,379,475 | 876,472,062 | 9,016,798 | 3,858,978 | 876,503,699 | 4,097,403 |
| Total (note 3) | SAMN10492705 | 204,108 | 897,855,544 | 736,676,981 | 15,200,441 | 17,592,488 | 865,062,615 | 81,123,968 |
Notes:
-
Total of African American and African Others; see population descriptions.
-
Total of East Asian and Other Asian; see population descriptions.
-
Total of unique subjects and excluding African and Asian redundant counts above.
Column descriptions:
Output Population - see ALFA computed populations
BioSample ID - population BioSample accession ID
Subjects - unique subject count by population
Total Site Count - total unique variant sites reported
MAF = 0 - site homozygous for the reference allele and no variant allele detected from the current subject sample size; possibly rare if subject size > 100
MAF >= 0.01 - common variant with MAF >= 0.01
0.01 > MAF >= 0.001 - rare variants
MAF < 0.001 - ultra rare variants
Singleton - minor allele is found once