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Table 5 Concordance of variants associated with SLB resistance at resample model inclusion probabilities (RMIPs) of 0.05 and 0.25 from five GWAS analyses

From: Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population

Comparisons GWAS modelsa RMIP ≥ 0.05 RMIP ≥ 0.25
No. of all significant SNPsb Proportion of overlapped SNPs (%)c No. of all significant SNPs Proportion of overlapped SNPs (%)c
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GWAS marker density B vs. C 326 (151,175) 26 36 38 45 (25,20) 13 13 13
D vs. E 393 (201,192) 22 34 39 54 (28,26) 11 11 15
Genetic map density C vs. E 367 (175,192) 14 21 23 46 (20,26) 9 9 9
B vs. D 352 (151,201) 25 29 35 53 (25,28) 26 28 28
GWAS and genetic marker density C vs. D 376 (175,201) 13 21 22 48 (20,28) 4 8 8
B vs. E 343 (151,192) 7 13 15 51 (25,26) 4 4 4
GWAS and genetic marker density and P-value A vs. E 437 (245,192) 6 12 15 52 (26,26) 4 4 4
  1. aSee Table 1 for details of each GWAS model.
  2. bTotal number of all the significant SNPs from a pair of analyses is shown outside of parentheses and numbers of significant SNPs from each analysis considered separately are inside the parenthesis.
  3. cProportion of overlapped SNPs was estimated as the total number of overlapped SNPs from a pair of analyses/total number of all the significant SNPs from the two analyses.
  4. Comparisons show the input(s) that differed in each pair of GWAS comparisons.