90555c79f13bedec650b761a878c23a9620001bc kuhn Tue Dec 3 13:20:04 2019 -0800 replaced the word thousand with ,000 so it reads better. dropped space in rsIDs diff --git src/hg/makeDb/trackDb/human/dbSnp153Composite.html src/hg/makeDb/trackDb/human/dbSnp153Composite.html index 8699190..9d80635 100644 --- src/hg/makeDb/trackDb/human/dbSnp153Composite.html +++ src/hg/makeDb/trackDb/human/dbSnp153Composite.html @@ -17,59 +17,59 @@ 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). </p> <p> This track includes four subtracks of variants: <ul> <li><b>All dbSNP (153)</b>: the entire set (683 million for hg19, 702 million for hg38) </li> <li><b>Common dbSNP (153)</b>: approximately 15 million variants with a minor allele frequency (MAF) of at least 1% (0.01) in the 1000 Genomes Phase 3 dataset. Variants in the Mult. subset (below) are excluded. </li> - <li><b>ClinVar dbSNP (153)</b>: approximately 455 thousand variants mentioned in ClinVar. + <li><b>ClinVar dbSNP (153)</b>: approximately 455,000 variants mentioned in ClinVar. <b>Note:</b> that includes both benign and pathogenic (as well as uncertain) variants. Variants in the Mult. subset (below) are excluded. </li> <li><b>Mult. dbSNP (153)</b>: variants that have been mapped to multiple chromosomes, for example chr1 and chr2, raising the question of whether the variant is really a variant or just a difference between duplicated sequences. There are some exceptions in which a variant is mapped to more than one reference sequence, but not culled into this set: <ul> <li>A variant may appear in both X and Y pseudo-autosomal regions (PARs) without being included in this set. </li> <li>A variant may also appear in a main chromosome as well as an alternate haplotype or fix patch sequence assigned to that chromosome. </li> </ul> </li> </ul> </p> <p> A fifth subtrack highlights coordinate ranges to which dbSNP mapped a variant but with genomic coordinates that are not internally consistent, i.e. different coordinate ranges were provided when describing different alleles. This 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: <ul> - <li><b>Map Err (153)</b>: around 120 thousand mappings of 55 thousand distinct rs IDs for hg19 - and 149 thousand mappings of 86 thousand distinct rs IDs for hg38. + <li><b>Map Err (153)</b>: around 120,000 mappings of 55,000 distinct rs IDs for hg19 + and 149,000 mappings of 86,000 distinct rs IDs for hg38. </ul> </p> <h2>Interpreting and Configuring the Graphical Display</h2> <p> 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. </p><p> 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