58f9a8971053e464cfefcfff018e491cae5dd8f3 dschmelt Mon Aug 30 11:27:36 2021 -0700 Setting width of Tables at b0b's request No RM diff --git src/hg/makeDb/trackDb/human/dbSnp153Composite.html src/hg/makeDb/trackDb/human/dbSnp153Composite.html index 4565c43..09a717b 100644 --- src/hg/makeDb/trackDb/human/dbSnp153Composite.html +++ src/hg/makeDb/trackDb/human/dbSnp153Composite.html @@ -186,31 +186,31 @@
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 (dbSnp153.bb) | # in hg19 | # in hg38 | description |
---|---|---|---|
clinvar | 454678 | 453996 | Variant is in ClinVar. |
clinvarBenign | 143864 | 143736 | Variant is in ClinVar with clinical significance of benign and/or likely benign. |
revStrand | 3813702 | 4532511 | 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 | 3272116 | 3360435 | The reference genome allele is not the major allele in at least one project. | 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 | 10755 | 10888 | 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 | 5998 | 6216 | Variation class/type is inconsistent with alleles mapped to this genome assembly. |