Population comparison

Answer: 

This help page is for both the population comparison table and comparison image. Variation sources are described in this document.

POPULATION COMPARISON TABLE

For the choosen transcript, the table lists the allele at each variant position in different individuals or strains.

To configure the individuals, breeds or strains displayed, or types of variation (such as intronic, non-synonymous, etc.) click on configure this page at the left of the page. By default, not all intronic variants are shown. This can be changed with the "Context" roll-down menu in the configure page panel. Any selections in the configure page menu will affect the comparison image as well as the table.

COMPARISON IMAGE

This graphical display shows one transcript and variation data in genomic context across individuals or strains.

Variation Track

This track displays all variations in this genomic region. These are colour-coded as shown in the variation legend at the bottom of the page.

Transcript for Each Individual, Breed or Strain

The transcript is drawn for each individual, breed, or strain selected in the configure this page menu. Under this, a grey bar shows sequence (if available) for that individual (breed or strain). A dark grey bar indicates high coverage in that genomic region. A light grey bar shows low coverage. (For example, in an individual, high coverage would signify both strands of the genome sequenced, and low coverage would only be one strand sequenced). Clicking on a grey bar produces a pop-up with detailed information on the coverage depth and positioning.

Coloured Boxes Under Each Transcript

Boxes underneath each individual, breed, or strain indicate the presence of an alternative allele in a variant position. Click on any box for more details on that variation. Amino acids are written in single-letter code format within the boxes, if the variations map to coding regions. Changes for non-synonymous single nucleotide polymorphisms (SNPs) are indicated with a forward slash (e.g. S/C denotes a change from Serine to Cysteine). A SNP affecting a STOP codon either by introducing a new one (e.g. A/*) or removing an existing one (e.g. */Q) is indicated by a red box, and the STOP codon by an asterisk (*).

Allele Position Boxes

Below the transcripts, each variation locus that falls within the transcript is shown by a hollow box outlined with a colour that corresponds to the variant's effect or position on the transcript. The colours are described in the variation legend. The possible alleles (nucleotides) for each variation are written in the corresponding box. The first allele is the one in the reference sequence assembly, and the second, the other possible allele reported. For example, a box with A/G indicates at that position, A is the reference allele, but G is a potential allele for that individual, breed or strain. Click on any hollow box for more information.

Haplotype Display

Each allele position box described above (i.e. hollow box showing nucleotides) corresponds to a green block in the reference sequence track below. The aim of this display is to compare the haplotype block structure in the reference sequence, each individual, breed, or strain selected. Where the allele matches the reference nucleotide sequence, the boxes are filled in green. (The reference allele is the first nucleotide in the corresponding allele position box). Where the alleles differ from the reference, the boxes are filled with purple. If both alleles are known in an individual, breed, or strain at a heterozygous position, the box is striped, green and purple.