Description
This track contains information about single nucleotide polymorphisms
and small insertions and deletions (indels) — collectively Simple
Nucleotide Polymorphisms — from
dbSNP
build 150, available from
ftp.ncbi.nlm.nih.gov/snp.
Three tracks contain subsets of the items in this track:
- Common SNPs(150): SNPs that have a minor allele frequency
of at least 1% and are mapped to a single location in the reference
genome assembly. Frequency data are not available for all SNPs,
so this subset is incomplete.
- Flagged SNPs(150): SNPs flagged as clinically associated by dbSNP,
mapped to a single location in the reference genome assembly, and
not known to have a minor allele frequency of at least 1%.
Frequency data are not available for all SNPs, so this subset may
include some SNPs whose true minor allele frequency is 1% or greater.
- Mult. SNPs(150): SNPs that have been mapped to multiple locations
in the reference genome assembly. There are very few SNPs in this category
because dbSNP has been filtering out almost all multiple-mapping SNPs since
build 149.
The default maximum weight for this track is 1, so unless
the setting is changed in the track controls, SNPs that map to multiple genomic
locations will be omitted from display. When a SNP's flanking sequences
map to multiple locations in the reference genome, it calls into question
whether there is true variation at those sites, or whether the sequences
at those sites are merely highly similar but not identical.
The remainder of this page is identical on the following tracks:
- Common SNPs(150) - SNPs with >= 1% minor allele frequency (MAF), mapping
only once to reference assembly.
- Flagged SNPs(150) - SNPs < 1% minor allele frequency (MAF) (or unknown),
mapping only once to reference assembly,
flagged in dbSnp as "clinically associated"
-- not necessarily a risk allele!
- Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly.
- All SNPs(150) - all SNPs from dbSNP mapping to reference assembly.
Interpreting and Configuring the Graphical Display
Variants are shown as single tick marks at most zoom levels.
When viewing the track at or near base-level resolution, the displayed
width of the SNP corresponds to the width of the variant in the reference
sequence. Insertions are indicated by a single tick mark displayed between
two |