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Table 3 Recombination crossover sites in YMMV genomes detected by RDP4

From: Genetic diversity and genome recombination in Yam mild mosaic virus isolates

 Parental sequences 
Event No.Found inRecombinantMajorMinorDetecting methodsaP values
I1NC1NN1NC2R G B M C7.741 × 10−13, 8.558 × 10−14, 6.872 × 10− 13, 2.670 × 10−3, 2. 442 × 10−3
II1CN1WX1NC3R B C S1.066 × 10−6, 6.842 × 10−10, 1.148 × 10−10, 3.226 × 10−5
III1NC2FX1WX3M C S 33.367 × 10−11, 4.606 × 10−13, 2.116 × 10−6, 5.180 × 10−7
IV1CN20WX1NC3R B M C4.927 × 10−3, 1.287 × 10−2, 6.484 × 10−6, 5.180 × 10− 7
  1. aRecombinant isolates identified by the recombination detecting programs, R (RDP), G (Geneconv), B (Bootscan), M (Maxchi), C (Chimaera), S (Siscan) and 3 (3seq) programs in RDP4 v.4.56. The analysis was carried out with default settings for the different detection methods and a Bonferroni corrected P values cut-off of 0.05. And the detected site with a Bonferroni corrected P values of less than 1 × 10− 6 was considered as a clear recombination site whilst a detected site with P values of grater than1 × 10− 6 as a tentative recombination sites. The P values obtained by different detection methods are shown in the last column of the table, where the bold font indicates that the P value of less than 1 × 10− 6