Build Summary
Release 2 Version: 20201027095038
January 6, 2021
Please visit ALFA project page for data access and additional information.
Input and Output Counts
| Input | Release 1 | Release 2 |
|---|---|---|
| Studies | 42 | 79 |
| Subjects | 98,494 | 192,710 |
| Genotypes | 551,345,630,054 | 5,762,708,417,353 |
| Genotypes Excluded | 689,601,274 (0.1%) | 70,905,472,368 (1.2%) |
| Output | Count |
|---|---|
| Total RefSNPs | 904,167,063 |
| Exist in dbSNP 153 | 587,734,538 |
| Novel | 316,432,525 |
| Input Assay Source | Subjects* |
|---|---|
| Array | 109,697 |
| Exome | 29,931 |
| Genome | 25,478 |
* 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 | 163,190 | 897,674,770 | 790,647,710 | 12,681,797 | 10,209,207 | 874,783,766 | 55,326,962 |
| African American | SAMN10492698 | 5,989 | 890,636,714 | 824,003,273 | 17,196,729 | 17,457,964 | 855,982,021 | 25,207,366 |
| African Others | SAMN10492696 | 211 | 889,747,124 | 867,277,986 | 16,180,269 | 6,288,869 | 867,277,986 | 6,669,925 |
| African (Note 1) | SAMN10492703 | 6,200 | 890,637,200 | 823,004,460 | 17,231,538 | 17,793,146 | 855,612,516 | 25,718,386 |
| South Asian | SAMN10492702 | 2,619 | 889,129,503 | 875,443,975 | 13,537,787 | 140,039 | 875,451,677 | 4,209,516 |
| East Asian | SAMN10492697 | 2,515 | 889,348,478 | 877,811,054 | 11,378,577 | 133,556 | 877,836,345 | 3,529,940 |
| Other Asian | SAMN10492701 | 1,000 | 889,147,573 | 880,606,177 | 8,492,026 | 41,240 | 880,614,307 | 2,584,569 |
| Asian (Note 2) | SAMN10492704 | 3,515 | 889,368,170 | 876,465,327 | 9,012,224 | 3,858,982 | 876,496,964 | 4,096,666 |
| Latin American 1 | SAMN10492699 | 817 | 889,286,501 | 869,906,237 | 12,609,493 | 6,770,469 | 869,906,539 | 6,683,030 |
| Latin American 2 | SAMN10492700 | 4,703 | 889,328,426 | 862,575,116 | 9,597,908 | 17,148,719 | 862,581,799 | 11,064,135 |
| Other | SAMN11605645 | 11,666 | 897,694,388 | 859,254,160 | 14,970,456 | 22,452,177 | 860,271,755 | 14,013,627 |
| Total (Note 3) | SAMN10492705 | 192,710 | 897,734,484 | 737,043,490 | 15,177,885 | 17,568,436 | 864,988,163 | 80,931,234 |
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
Data Subsets in ClinVar, GTR, dbGaP, and PubMed
RefSNP with ALFA frequency (ALFA RS Count) and percent (%) of total RS (Total) in ClinVar with clinical significance, in GTR as genetic markers, in dbGaP with association p-value, and cited in PubMed. VCF containing RS subsets are available on FTP
| Attributes | ALFA RS Count | Percent(%) | Total RS |
|---|---|---|---|
| ClinVar | 333,721 | 86 | 387,427 |
| GTR | 398 | 84 | 474 |
| GWAS Catalog (p-value < 10^-5) | 21,827 | 99 | 21,972 |
| Pubmed Cited | 202,156 | 87 | 231,502 |