Table 2

SNP calling measurements for Crossbow experiments using simulated reads from human chromosomes 22 and X

Chromosome 22

Chromosome X



True number of sites

Crossbow sensitivity

Crossbow precision

True number of sites

Crossbow sensitivity

Crossbow precision


All SNP sites

46,586

99.0%

99.1%

102,219

99.0%

99.6%

Only HapMap SNP sites

36,096

99.8%

99.9%

71,976

99.9%

99.9%

Only novel SNP sites

10,490

96.3%

96.3%

30,243

96.8%

98.8%

Only homozygous

14,858

98.7%

99.9%

NA

NA

NA

Only heterozygous

31,728

99.2%

98.8%

NA

NA

NA

Only novel het

6,967

96.6%

94.6%

NA

NA

NA

All other

39,619

99.4%

99.9%

NA

NA

NA


Sensitivity is the proportion of true SNPs that were correctly identified. Precision is the proportion of called SNPs that were genuine. NA denotes "not applicable" because of the ploidy of the chromosome.

Langmead et al. Genome Biology 2009 10:R134   doi:10.1186/gb-2009-10-11-r134

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