ALFA Track Settings
 
ALFA: Allele Frequency Aggregator

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Display data as a density graph:
All subtracks:
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 Configure 		 NCBI ALFA: African  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: African American  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: African Others  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: Asian  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: East Asian  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: European  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: Global  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: Latin American 1  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: Latin American 2  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: Other  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: Other Asian  ALFA: Allele Frequency Aggregator   Data format 
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 Configure 		 NCBI ALFA: South Asian  ALFA: Allele Frequency Aggregator   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

The NCBI ALlele Frequency Aggregator (ALFA) pipeline is developed to compute allele frequency for variants in dbGaP across approved un-restricted studies and to provide the data as open-access to the public through dbSNP. The goal of the ALFA project is to make frequency data from over 1M dbGaP subjects open-access in future releases to facilitate discoveries and interpretations of common and rare variants with biological impacts or causing diseases.

The initial release of ~100 thousand subjects included allele counts and frequency for 447 million rs site including 4 million novel ones aggregated from 551 billion genotypes. More information about ALFA can be found at https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/ and any questions about ALFA track data should be forwarded to <mailto:snp-admin@ncbi.nlm.nih.gov>.

Subtracks

This track contains data from 12 populations:

* ALFA data for African population

* ALFA data for African American population

* ALFA data for African Others population

* ALFA data for Asian population

* ALFA data for East Asian population

* ALFA data for European population

* ALFA data for Global population

* ALFA data for Latin American 1 population

* ALFA data for Latin American 2 population

* ALFA data for Other population

* ALFA data for Other Asian population

* ALFA data for South Asian population

 

Display Conventions and Configuration

Labels

The variant label is the dbSNP reference SNP ID (rsid).

Mouseover

The mouseover (displayed when the mouse is hovered over a variant) shows the following:

  • Chromosome
  • position
  • Reference allele and frequency
  • Alternate allele and frequency

 

Detail Page

The detail page contains the following:

  

Variant Colors

The colors indicate the alternate allele frequencies.

  • red: alternate allele frequency falls in [0.5, 1]
  • blue: alternate allele frequency falls in [0.4, 0.5)
  • violet: alternate allele frequency falls in [0.3, 0.4)
  • light violet: alternate allele frequency falls in [0.2, 0.3)
  • light azure: alternate allele frequency falls in [0.1, 0.2)
  • brown: alternate alelle frequency falls in [0, 0.1)