Variation data in fungi
(a) How many species in Ensembl Fungi have variation data?
(b) Select Fusarium oxysporum and search for FOXG_13574T0 gene. One of its upstream variants is SNP tmp_10_6610. What are the possible alleles for this polymorphic position? Which one is on the reference genome?
(c) What is the most frequent allele at this position?
(d) Which samples have the genotypes C|T and T|T?
(a) Go to Ensembl Fungi, click on View full list of all species. Click on the upward triangle next to the Variation database column to sort the table by species with variation data.
The table shows that we have eight fungi species currently with variation databases.
(b) Click on Fusarium oxysporum in the table and on the species page search for FOXG_13574T0. From the Gene tab, click on Variant table and then scroll down to find tmp_10_6610 or use the table search box to find it.
The alleles are C/T, where C is the reference allele.
(c) Click on tmp_10_6610 in the table to open the Variant tab. Then click on Genotype Frequency from the menu on the left hand side of the page.
The most frequent allele at this position is C with a frequency of 0.850.
(d) Click on Sample genotypes in the left menu.
The table shows that sample 909454 has the C|T genotype and 909455 has the T|T genotype.