7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 jnavarr5 Mon Oct 7 10:55:15 2019 -0700 Updating http to https for hg19, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/snp151Common.html src/hg/makeDb/trackDb/human/snp151Common.html index 82f1c34..86dca09 100644 --- src/hg/makeDb/trackDb/human/snp151Common.html +++ src/hg/makeDb/trackDb/human/snp151Common.html @@ -15,31 +15,31 @@ Allele counts from all submissions that include frequency data are combined when determining MAF, so for example the allele counts from the 1000 Genomes Project and an independent submitter may be combined for the same variant.

dbSNP provides download files in the Variant Call Format (VCF) that include a "COMMON" flag in the INFO column. That is determined by a different method, and is generally a superset of the UCSC Common set. dbSNP uses frequency data from the -1000 Genomes Project +1000 Genomes Project only, and considers a variant COMMON if it has a MAF of at least 0.01 in any of the five super-populations:

In build 151, dbSNP marks approximately 38M variants as COMMON; 23M of those have a global MAF < 0.01. The remainder should be in agreement with UCSC's Common subset.

The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common