For hg38 (GRCh38), approximately 667 million distinct variants (RefSNP clusters with rs# ids) have been mapped to over 702 million genomic locations including alternate haplotype and fix patch sequences. dbSNP remapped variants from hg38 to hg19 (GRCh37); approximately 658 million distinct variants were mapped to over 683 million genomic locations including alternate haplotype and fix patch sequences (not all of which are included in UCSC's hg19).
-This track includes four subtracks: +This track includes four subtracks of variants:
+A fifth subtrack highlights coordinate ranges to which dbSNP mapped a variant but with genomic +coordinates that are not self-consistent, i.e. different coordinate ranges were provided when describing different alleles, which can occur due to a bug with mapping variants from one assembly sequence to another when there is an indel difference between the assembly sequences: +
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
@@ -178,194 +185,194 @@
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:
Interesting and anomalous conditions noted by UCSC
| keyword in data file (dbSnp153.bb) | # in hg19 | # in hg38 | description | ||
|---|---|---|---|---|---|
| clinvar | -454656 | -453954 | +454674 | +453990 | Variant is in ClinVar. |
| clinvarBenign | -143844 | -143696 | +143860 | +143730 | Variant is in ClinVar with clinical significance of benign and/or likely benign. |
| clinvarConflicting | 7932 | 7950 | Variant is in ClinVar with reports of both benign and pathogenic significance. | ||
| clinvarPathogenic | 96242 | 95262 | Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic. | ||
| commonAll | -12178426 | -12430253 | +12184226 | +12438325 | Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies. |
| commonSome | -20534330 | -20893174 | +20540882 | +20902602 | Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies. |
| diffMajor | -1377402 | -1398591 | +1377817 | +1399094 | Different frequency sources have different major alleles. |
| overlapDiffClass | -106940656 | -109838613 | +107003090 | +109991096 | This variant overlaps another variant with a different type/class. |
| overlapSameClass | -16890303 | -17228657 | +16910407 | +17281744 | This variant overlaps another with the same type/class but different start/end. |
| rareAll | -662571654 | -681626796 | +662595470 | +681685476 | Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in all projects reporting frequencies, or has no frequency data. |
| rareSome | -670927558 | -690089717 | +670952126 | +690149753 | Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in some, but not all, projects reporting frequencies, or has no frequency data. |
| revStrand | -3813390 | -4512600 | +3813467 | +4532270 | Alleles are displayed on the + strand at the current position. dbSNP's alleles are displayed on the + strand of a different assembly sequence, so dbSNP's variant page shows alleles that are reverse-complemented with respect to the alleles displayed above. |
while others may indicate that the reference genome contains a rare variant or sequencing issue:
| keyword in data file (dbSnp153.bb) | # in hg19 | # in hg38 | description | ||
|---|---|---|---|---|---|
| refIsAmbiguous | 101 | 111 | The reference genome allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G', or 'N' for 'any base'). | ||
| refIsMinor | -3269451 | -3356557 | +3271878 | +3360159 | The reference genome allele is not the major allele in at least one project. |
| refIsRare | -135265 | -158562 | +136452 | +160723 | The reference genome allele is rare (i.e. allele frequency < 1%). |
| refIsSingleton | -36709 | -48859 | +37783 | +50865 | 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 (dbSnp153.bb) | # in hg19 | # in hg38 | description | ||
|---|---|---|---|---|---|
| altIsAmbiguous | -10747 | -10873 | +10754 | +10880 | 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 | -5701 | -5864 | +5995 | +6206 | Variation class/type is inconsistent with alleles mapped to this genome assembly. |
| clusterError | -113678 | -126973 | +114685 | +128109 | This variant has the same start, end and class as another variant; they probably should have been merged into one variant. |
| freqIsAmbiguous | -7649 | -7749 | +7656 | +7756 | At least one allele reported by at least one project that reports frequencies contains an IUPAC ambiguous base. |
| freqNotRefAlt | -16950 | -30615 | +17684 | +32150 | 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 | -561309 | -132015 | +562157 | +132051 | 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,