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Table 1 Performance of the Altools platform (detection of polymorphisms). Statistical analysis of Altools polymorphism calling was carried out at five simulated coverage levels

From: Altools: a user friendly NGS data analyser

Coverage 4x 10x 20x 40x 100x
dgwsim generated polymorphisms 121,388 122,074 121,368 121,540 121,638
dgwsim generated SNPs 107,054 107,411 106,766 107,372 107,277
dgwsim generated indels 14,334 14,663 14,602 14,168 14,361
Altools total called SNPs 35,714 81,647 102,493 105,164 105,580
Altools correctly called SNPs 35,650 81,482 102,274 104,910 105,243
Altools false positive SNPs 64 165 219 254 337
Altools total called indels 3049 8307 11,134 11,542 11,657
Altools correctly called indels 3040 8280 11,112 11,503 11,621
Altools false positive indels 9 27 22 39 36
PPV      
SNPs 1.00 1.00 1.00 1.00 1.00
Indels 0.33 0.76 0.96 0.98 0.98
Sensitivity      
SNPs 1.00 1.00 1.00 1.00 1.00
Indels 0.21 0.56 0.76 0.81 0.81
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