Build Summary
Release Version: 20200227123210
March 10, 2020
Input and Output Counts
| Input | Count |
|---|---|
| Studies | 42 |
| Subjects | 98,494 |
| Genotypes | 551,345,630,054 |
| Genotypes Excluded | 689,601,274 (0.1%) |
| Output | Count |
|---|---|
| Total RefSNPs | 446,909,594 |
| Exist in dbSNP 153 | 442,539,572 |
| Novel | 4,370,022 |
| Input Assay Source | Subjects* |
|---|---|
| Exome | 23,224 |
| Genomes | 5,621 |
| SNP Arrays | 87,232 |
* Subject counts for different assay source can be overlapping.
| Output Population | BioSample ID | Subjects | Total Site Count | MAF = 0 | MAF >= 0.01 | 0.01 > MAF >= 0.001 | MAF < 0.001 | Singleton |
|---|---|---|---|---|---|---|---|---|
| European | SAMN10492695 | 82,475 | 445,828,538 | 413,136,224 | 8,616,684 | 4,946,828 | 432,265,026 | 15,684,278 |
| African American | SAMN10492698 | 3,555 | 445,809,613 | 428,151,478 | 17,105,759 | 545,913 | 428,157,941 | 5,164,009 |
| African Others | SAMN10492696 | 114 | 445,691,099 | 438,202,529 | 7,470,894 | 17,676 | 438,202,529 | 3,251,737 |
| African (Note 1) | SAMN10492703 | 3,669 | 445,809,758 | 427,767,482 | 17,490,705 | 544,974 | 427,774,079 | 5,249,871 |
| East Asian | SAMN10492697 | 153 | 445,720,538 | 442,454,208 | 3,246,297 | 20,033 | 442,454,208 | 1,646,717 |
| South Asian | SAMN10492702 | 2,459 | 445,079,683 | 440,460,693 | 4,603,791 | 7,562 | 440,468,330 | 2,361,549 |
| Other Asian | SAMN10492701 | 84 | 445,465,162 | 442,628,722 | 2,828,952 | 7,488 | 442,628,722 | 1,741,650 |
| Asian (Note 2) | SAMN10492704 | 237 | 445,757,479 | 441,170,505 | 4,548,632 | 38,342 | 441,170,505 | 2,079,552 |
| Latin American 1 | SAMN10492699 | 354 | 3,176,558 | 1,403,168 | 1,752,470 | 20,920 | 1,403,168 | 254,597 |
| Latin American 2 | SAMN10492700 | 3,801 | 3,194,467 | 1,173,905 | 1,949,095 | 68,415 | 1,176,957 | 206,300 |
| Other | SAMN11605645 | 5,499 | 445,829,307 | 434,443,847 | 10,314,708 | 450,584 | 435,064,015 | 3,604,601 |
| Total (Note 3) | SAMN10492705 | 98,494 | 445,835,693 | 404,944,004 | 9,245,548 | 8,393,159 | 428,196,986 | 18,638,600 |
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(%) of Total | Total RS |
|---|---|---|---|
| ClinVar | 229963 | 59 | 387427 |
| GTR | 366 | 77 | 474 |
| GWAS Catalog (p-value < 10^-5) | 21494 | 98 | 21972 |
| Pubmed Cited | 188809 | 82 | 231502 |