GVS: Genome Variation Server 144
6
Navigating the Map

The map can be accessed from three locations:

1. the "browse" button on the home page, followed by a chromosome choice

2. the map icon on the "Select Population(s)" page

3. the "display snp summary" button on the "Select Population(s)" page (the map pops up in a new window)

In all cases, the locations of genes are displayed in the "gene model" bar. If the map comes from the "display snp summary" button, or if the chromosome range is not too large, the coding and untranslated regions of the sequence are shown for each transcript.

The small green arrows move the region right or left by 50% of the range; the large arrows, by 95%. The zoom buttons expand and contract the region by a factor of 2. For most modern browser/operating system combinations, it is possible to drag the map horizontally by starting the drag on or below the gene-model bar, and to select a region for expansion by starting the drag above the gene-model bar and ending the drag below the bar. Keystrokes will work on some systems. The 'j' and 'k' keys will move the region left or right by a small amount. The 'i' and 'm' keys will zoom in and out about the point at which the mouse is placed. (This key zoom feature works with mouse events, so if you want to zoom about the same point several times, it is necessary to move the mouse a bit each time a new map comes up, in order to record the mouse position.)

Clicking on a gene label initiates a genotype search for that gene. The gene labels can be hidden by clicking the "hide gene names" button.

Clicking the "show SNP density" button brings up a display of the number of SNPs in a bin, with the bin size depending on the map scale.

If the map comes from the "display snp summary" button, or if the chromosome range is not too large, the locations of SNPs are shown above the gene model. If the region is less than 10,000 bases, the SNPs are drawn with a thick line, and overlapping SNPs are separated. In this case, for most modern browser/operating system combinations, it is possible to roll the mouse over a SNP line and see the rs ID.

If the map comes from the "display snp summary" button, the SNP display is somewhat different from that of the other two cases. Whereas in the other cases all SNPs with genotypes are shown, in the summary map only those SNPs for the particular population/submitter combination (and other parameters set) are shown. Here the SNP line lengths are proportional to the SNP frequency in the population chosen (with a few pixels added so low-frequency SNPs are visible).
 
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