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Table 13 Positive calling rate and sensitivity

From: Comparing a few SNP calling algorithms using low-coverage sequencing data

 

Empirical truth

SNV

Not SNV

Program’s calling results

called as SNV

A

B

 

called as Reference (i.e., not SNV)

C

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  1. 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).
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BMC Bioinformatics

ISSN: 1471-2105

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