a33a189301f539896d9df28df9008b50f65d757f lrnassar Fri Aug 2 12:09:41 2024 -0700 Fixing up grammar, feedback from CR refs #34174 diff --git src/hg/makeDb/trackDb/evaSnpContainer.html src/hg/makeDb/trackDb/evaSnpContainer.html index 7d7add9..51306ef 100644 --- src/hg/makeDb/trackDb/evaSnpContainer.html +++ src/hg/makeDb/trackDb/evaSnpContainer.html @@ -37,77 +37,77 @@

Variants can be filtered using the track controls to show subsets of the data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or by color, which bins the UCSC functional effects into general classes.

Mouse-over

Mousing over an item shows the ucscClass, which is the consequence according to the Variant Annotation Integrator, and the aaChange when one is available, which is the change in amino acid in HGVS.p terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID separated by spaces describing all possible AA changes.

Multiple items may appear due to different variant predictions on multiple gene transcripts. -For all organisms the gene models used were the NCBI RefSeq curated when available, if not then +For all organisms, the gene models used were the NCBI RefSeq curated when available, if not then ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible.

Track colors

Variants are colored according to the most potentially deleterious functional effect prediction according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section below.

Color Variant Type

Protein-altering variants and splice site variants

Synonymous codon variants

Non-coding transcript or Untranslated Region (UTR) variants

Intergenic and intronic variants

Color	Variant Type
	Protein-altering variants and splice site variants
	Synonymous codon variants
	Non-coding transcript or Untranslated Region (UTR) variants
	Intergenic and intronic variants

Sequence ontology (SO)

Sequence Ontology (SO)

Variants are classified by EVA into one of the following sequence ontology terms:

substitution — A single nucleotide in the reference is replaced by another, alternate allele
deletion — - One or more nucleotides is deleted. The representation in the database is to + One or more nucleotides are deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A maybe be represented as Ref = GA and Alt = G.
insertion — - One or more nucleotides is inserted. The representation in the database is to + One or more nucleotides are inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the - Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe + Alternate Allele field (Alt). E.g. a variant that is an insertion of a T may be represented as Ref = G and Alt = GT
delins — - Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of + Similar to a tandem repeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC.
multipleNucleotideVariant — More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC.
sequence alteration — A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet.

Methods

Data were downloaded from the European Variation Archive EVA EVA Release 6 MakeDoc.

Data Access

-Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, +Note: It is not recommended to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry.

The data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from our download server. Use the corresponding version number for the track of interest, e.g. evaSnp6.bb.