allele frequency threshold

[Huiping Chen]

Hi, I setup allele frequency threshold at 20%, but the consensus sequence did not show alleles in SNV at 20%, only displayed alleles with frequency more than or equal to 33.3%. I wonder why the alleles at 20% can not be displayed in the consensus sequence. thanks.

Best regards,

Huiping

[igv-help]

Sorry but I don't understand your question,   but the consensus sequence calculation is described here.  Perhaps this will help.

https://igv.org/doc/desktop/#UserGuide/tracks/alignments/viewing_alignments_basics/#consensus-sequence

[igv-help]

Apologies the website is encoding the "#" symbol  in the doc link,  if you get a page not found  try replacing the "%23" in the link in your browser.   I've pasted the contents of that link below

https://igv.org/doc/desktop/#UserGuide/tracks/alignments/viewing_alignments_basics/#consensus-sequence

The menu item "Copy consensus sequence" calculates the consensus sequence for the region in view and copies the information to the clipboard. The method for calculating the consensus is taken from Cavener, Nucleic Acids Res. 15, 1353-1361, 1987.

1. If the frequency of a single nucleotide at a specific position is greater than 50% and greater than twice the number of the second most frequent nucleotide it is assigned as the consensus nucleotide.

2. If the sum of the frequencies of two nucleotides is greater than 75% (but neither meet the criteria for a single nucleotide assignment) they are assigned as co-consensus nucleotides.

3. If no single nucleotide or pair of nucleotides meets the criteria, assign an 'N'.