Table 13

Positive calling rate and sensitivity
Empirical truth
SNV Not SNV
Program’s calling results called as SNV A B
called as Reference (i.e., not SNV) C --

For a specific calling program (e.g., SOAPsnp), A is the number of SNVs identified as an empirical truth (i.e., called by at least 3 calling programs) and also called by this calling program; B is the number of SNVs identified as an empirical truth, but not called by this calling program; C is the number of SNVs called by this calling program, but is not an empirical truth. Positive calling rate is calculated as A/(A + B); sensitivity is calculated as A/(A + C).

Yu and Sun

Yu and Sun BMC Bioinformatics 2013 14:274   doi:10.1186/1471-2105-14-274

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