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Table 5 Comparison of several SNP filtering criteria and ADT design scores in true-positive and false-positive SNPs

From: Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms

SNP No of SNPs ADT design score Average quality score of reference SNP quality score of reference SNP mapping quality score Read mapping depth Folded variant frequency
True-positive 2,765 0.974 ± 0.050(a) 54.9 ± 9.4 59.2 ± 6.6 34.3 ± 1.6 18.4 ± 9.3 0.39 ± 0.11
False-positive 2,655 0.971 ± 0.053 54.3 ± 10.1 59.1 ± 7.1 33.7 ± 2.0 31.7 ± 18.0 0.34 ± 0.11
P value of t test   0.0597 0.0136* 0.4553 <0.0001** <0.0001** <0.0001**
  1. (a) average ± standard deviation; * and ** represent statistical significance at 0.05 and 0.01 probability level, respectively.