What is the definition of consensus call

Question

[xuzhougeng]

I just start a mapping-by-sequencing project, but I was confused with consensus call.

In order to find mutation with SHOREmap, I have to provide the SHOREmap extract or SHOREmap backcross with consensus call information. The program tutorial tell me that I should use 11_converted_consen.txt . I want to know what is the definition of *consensus call *.

Is that means the "snp" with many reads supporting?

Answer 1

[xuzhougeng]

I find a definition of consensus sequence.

consensus sequence

a sequence of NUCLEOTIDES or AMINO ACIDS that is used to describe a number of related but not identical sequences. It is compiled by inserting the nucleotide occurring most often at each position in the real sequences. -- Collins Dictionary of Biology, 3rd ed. © W. G. Hale, V. A. Saunders, J. P. Margham 2005

So, consensus call is the output produced by consensus caller to find consensus sequences. And we can find variation(such as snp) in this output file.

[BioinfGuru]

Example:

seq1 AGTC seq2 AGTT seq3 GGGT cons AGTT

The variations are then found by comparing seq1,2 and 3 against the consensus