Summary Information for refSNPs

The NCBI genome map viewer can be configured to supply additional information about elements in the master map by selecting verbose mode in the display settings dialog box.

When the "SNP" map is selected as the master map, the user is presented with a graphical summary of several properties of the SNP in a display that looks like this:

rs999991
rs999992
rs999993
rs999994
rs999995

In silico map results

The quality of the SNP is computed from mapping and validation data. The current set of map icons and their meanings are:

Map	Meaning
	Marker mapped to unique position in the genome. Markers mapped to two contigs on the same chromosome will also receive this icon, on the assumption that the contigs might not have been joined during sequence assembly.
	Marker mapped to multiple positions in the genome. Markers mapped to 2 to 10 different locations of the genome will receive this warning icon. Markers mapped to more than 10 locations will not be annotated on human genome sequence, nor will they be included in the genome map views.
	Markers that have been WITHDRAWN in dbSNP as a duplicated gene region or experimental artifact will be flagged with this WITHDRAWN icon. Evidence for withdrawing the marker can be found in the dbSNP refSNP report for the marker.
	This marker is not currently mapped to any genome location.

Gene region / functional classification

Markers placed on the sequence map are examined for neighboring gene features (gene, mRNA, CDS, and exon). Markers that satisfy the conditions below are considered a member of the set of markers associated the the gene, and each is assigned a functional classification depending on its particular location in the gene region:

Gene	Meaning
	LOCUS: Any part of the marker position on sequence map is within a 2kb interval 5' of the most 5' feature of gene (CDS, mRNA, gene), OR the marker position is within a 500 base interval 3' of the most 3' feature of the gene. Both strands of sequence are examined for gene features, so a marker can potentially be a variation on multiple genes at a single location.
	TRANSCRIPT: Any part of marker position overlaps with mRNA location (or overlaps with UTR/intron and mRNA feature is missing), BUT marker position is not within the coding region of the transcript.
	CODING: Any part of the marker position overlaps with a coding sequence (CDS) region (or overlaps with exon region in the unlikely case an exon is annotated but CDS is missing).
	The marker is not within the gene locus (as defined above) for any annotated gene.
	The marker is not within a transcript region for any annotated gene.
	The marker is not within a coding region for any annotated gene.

Marker heterozygosity

This 0 – 100% scale indicates the average heterozygosity as the range avg_het±2[SE(avg_het)], where SE(avg_het) is the standard error of the estimator. Thus the graph shows an approximate 95% confidence interval for the marker.

Het	Meaning
	No allele frequencies or measures of observed heterozygosity were submitted for this marker.
	Average heterozygosity shown as a 95% confidence interval (0.26 – 0.30). The estimate has a small standard error.
	Average heterozygosity shown as a 95% confidence interval (0.00 – 0.40) The estimate has a large standard error.

Quality Information

This scale distinguishes validated markers () from unvalidated ones (). Viewed as a vertically stacked histogram, the width of each scale reports the likelihood that a marker is real as defined by the submitter. This likelihood is based on validation experiments conducted by the submitter for each batch of reported markers, where the success rate for a batch is defined as 1 minus the false positive rate. Scale probabilities are:

Validation	Meaning
	Marker has been validated by independent resequencing.
	Unvalidated marker: success rate > 95%
	Unvalidated marker: success rate > 90%
	Unvalidated marker: success rate > 80%

Other Information

	Meaning
	Individual genotypes have been submitted to dbSNP for this marker.
	Links have been established between the dbSNP marker and a submitter website or database. These resources can provide additional information about the quality of the marker or its phenotypic effects for the organism or gene.