Get a list of SNPs/variants between 2+ varieties within a region of interest.¶

Example:

Region of interest: LcChr4:1875000-2075000
Germplasm of Interest: ILL 8006, CDC Milestone

Step #1: Go to the Lentil Genotype Matrix Tool¶

Go to https://knowpulse.usask.ca

Click on “Genotypes” at the top of the page. This will scroll you down to the genotypes section.

Click on “Lentil Genotypes” to access the Lentil Genotype Matrix Tool.

Step #2: Find genotypic data for your reference germplasm¶

Enter the name of each germplasm you are interested in by typing it in the textfield labelled germplasm. Then check the correct species is selected to the right of the textbox. To add more then one germplasm click the green + button.

For this example, Enter “ILL 8006” in the top germplasm textfield. You will notice that it autocompleted as you type.

Then click the green + button and enter “CDC Milestone” in the second textfield which appears.

Each time you click the green + button or search, the genotypic data for the listed germplasm will be shown.

Step #3: Restrict the Sequence Variants to polymorphic between your germplasm¶

Underneath germplasm, there is a filter to restrict to polymorphic variants. This filter compares two germplasm and only shows variants with different genotypic calls.

For our example, we would select ILL 8006 in the first drop down and CDC Milestone in the second drop-down to see only sequence variants with differing genotypes (i.e polymorphic variants) between these two germplasm.

Click Search to see the results.

Step #4: Restrict to you trait-implicated Region of the Genome.¶

The second section of the filter criteria available for the genotype matrix allows you to enter the region of the genome you are interested in. Once you click search, the genotype matrix will only show sequence variants found in this region.
In our example, the region of interest is LcChr4:1875000-2075000. To enter this we place LcChr4 for the Sequence Name, 1875000 for the start position and 2075000 for the end position.

Step #5: (Optionally): Restrict to specific variants.¶

Say you are interested in a specific set of variants and would like to see that subset.
You can enter the specific variant names by expanding the Additional Filter criteria section then clicking Search.