How can we know if a variant is in trans or cis when analysing a BAM file by IGV. In this example, the author says that both variants are in cis, How he knows
Taken from here https://www.researchgate.net/figure/Determination-of-cis-vs-trans-orientation-using-next-generation-sequencing-NGS-The_fig4_281852728
cis in Latin means on the near side, or in case of DNA on the same strand. trans in Latin means across, or in case of DNA on the opposite strand. They have the same meaning in chemistry for geometric isomers, except that there we have a double-bond plane that determines the sameness or the lack of it. This logic applies to other situations where the adjectives are used, like with gender.
Many thanks to all people who answer this.
So, in the image, two mutations are in cis when (as in the picture) each strand contains either both or neither of the mutations. OK, I got that. So, what happens when we only have one mutation per read and you find that your mutation is in 80% of the total number of read. Is this mutation in cis or in trans or does this question make no sense at all?
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they belong to the same read.
Text at the bottom of the image is important in this context (btw, never post image of a text): "The cis orientation is clearly visible, as each strand contains either both or neither of the mutations. " i.e both mutations are on the same strand whenever and wherever they occur.