SNVs and pure deletions are displayed as boxes covering the affected base(s). Pure insertions are drawn as single-pixel tickmarks between the base before and the base after the insertion.
Insertions and/or deletions in repetitive regions may be represented by a half-height box showing uncertainty in placement, followed by a full-height box showing the number of deleted bases, or a full-height tickmark to indicate an insertion. When an insertion or deletion falls in a repetitive region, the placement may be ambiguous. For example, if the reference genome contains "TAAAG" but some individuals have "TAAG" at the same location, then the variant is a deletion of a single A relative to the reference genome. However, which A was deleted? There is no way to tell whether the first, second or third A was removed. Different variant mapping tools may place the deletion at different bases in the reference genome. In order to reduce errors in merging variant calls made with different left vs. right biases, dbSNP made a major change in its representation of deletion/insertion variants in build 152. Now, instead of assigning a single-base genomic location at one of the A's, dbSNP expands the coordinates to encompass the whole repetitive region, so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's. In the track display, there will be a half-height box covering the first two A's, followed by a full-height box covering the third A, in order to show a net loss of one base but an uncertain placement within the three A's.
Variants are colored according to functional effect on genes annotated by dbSNP. Protein-altering variants and splice site variants are red, synonymous codon variants are green, and non-coding transcript or Untranslated Region (UTR) variants are blue.
On the track controls page, several variant properties can be included or excluded from the item labels: rs# identifier assigned by dbSNP, reference/alternate alleles, major/minor alleles (when available) and minor allele frequency (when available). Allele frequencies are reported independently by nine projects, as described by dbSNP:
Using the track controls, variants can be filtered by
While processing the information downloaded from dbSNP, UCSC annotates some properties of interest. These are noted on the item details page, and may be useful to include or exclude affected variants. Some are purely informational:
| keyword in data file (dbSnp152.bb) | # in hg19 | # in hg38 | description |
|---|---|---|---|
| clinvar | 409132 | 408665 | Variant is in ClinVar. |
| commonAll | 12757487 | 13027110 | Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies. |
| commonSome | 18901486 | 19258751 | Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies. |
| diffMajor | 823424 | 836327 | Different frequency sources have different major alleles. |
| overlapDiffClass | 99618012 | 102260850 | This variant overlaps another variant with a different type/class. |
| overlapSameClass | 14790469 | 15075710 | This variant overlaps another with the same type/class but different start/end. |
| revStrand | 3761191 | 4439534 | The orientation of the currently viewed reference genome sequence is different from the orientation of dbSNP's preferred top-level assembly sequence; alleles are presented on the forward strand of the currently viewed reference sequence. |
while others may indicate that the reference genome contains a rare variant or sequencing issue:
| keyword in data file (dbSnp152.bb) | # in hg19 | # in hg38 | description |
|---|---|---|---|
| refIsAmbiguous | 101 | 110 | The reference genome allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G', or 'N' for 'any base'). |
| refIsMinor | 2933684 | 3033691 | The reference genome allele is not the major allele in at least one project. |
| refIsRare | 150892 | 189809 | The reference genome allele is rare (i.e. allele frequency < 1%). |
| refIsSingleton | 45618 | 63804 | The reference genome allele has never been observed in a population sequencing project reporting frequencies. |
| refMismatch | 4 | 33 | The reference genome allele reported by dbSNP differs from the GenBank assembly sequence. This is very rare and in all cases observed so far, the GenBank assembly has an 'N' while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'. |
and others may indicate an anomaly or problem with the variant data:
| keyword in data file (dbSnp152.bb) | # in hg19 | # in hg38 | description |
|---|---|---|---|
| altIsAmbiguous | 10680 | 10807 | At least one alternate allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G'). For alleles containing more than one ambiguous base, this may create a combinatoric explosion of possible alleles. |
| classMismatch | 4808 | 5103 | Variation class/type is inconsistent with alleles mapped to this genome assembly. |
| clusterError | 106941 | 94310 | This variant has the same start, end and class as another variant; they probably should have been merged into one variant. |
| freqIsAmbiguous | 7635 | 7636 | At least one allele reported by at least one project that reports frequencies contains an IUPAC ambiguous base. |
| freqNotRefAlt | 23027 | 36306 | At least one allele reported by at least one project that reports frequencies does not match any of the reference or alternate alleles listed by dbSNP. |
| multiMap | 555144 | 130175 | This variant has been mapped to more than one distinct genomic location. |
dbSNP has collected genetic variant reports from researchers worldwide for over 20 years. Since the advent of next-generation sequencing methods and the population sequencing efforts that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline, web infrastructure, and download files. (Holmes et al.) The same challenges of exponential growth affected UCSC's presentation of dbSNP variants, so we have taken the opportunity to change our internal representation and import pipeline. Most notably, flanking sequences are no longer provided by dbSNP, since most submissions have been genomic variant calls in VCF format as opposed to independent sequences.
We downloaded dbSNP's JSON files available from ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b152/JSON/, extracted a subset of the information about each variant, and collated it into a bigBed file using the bigDbSnp.as schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page (dbSnpDetails.as schema).
The raw data underlying the UCSC Genome Browser track can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the track data files can be downloaded from the downloads server for hg38 and hg19 (dbSnp152.bb); the detailed variant properties can be downloaded from hgFixed (dbSnp152Details.tab.gz).
Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information.
https://www.biorxiv.org/content/10.1101/537449v3.full
https://www.ncbi.nlm.nih.gov/pubmed/30395293 PMC: PMC6323993
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783