![]() In this practical, we will try to find the genetic difference between ants from single queen and multiple queen colonies. Interestingly, this trait is genetically determined. The fire ant, Solenopsis invicta, is notable for being dimorphic in terms of colony organisation, with some colonies having one queen and other colonies having multiple queens. We will analyse subsets of whole-genome sequences of several fire ant individuals. Then we will find the positions where at least some of the individuals differ from the reference (and each other). First, we will map the reads from each individual to a reference assembly similar to the one created in the previous practical. ![]() There are several approaches to variant calling from short pair-end reads. Other classes include small insertions and deletions (known collectively as indels), as well as larger structural variants, such as large insertions, deletions, inversions and translocations. Commonly, people look at single nucleotide polymorphisms (SNPs, sometimes also known as single nucleotide variants, SNVs). Roddy Pracana and Yannick Wurm Introduction
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