Table 1 Predicted potential recombination events using different detection methods available in the RDP4 program
| Â | Breakpoint positions in the alignment | Â | P-Values for the detection methods in RDP4 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Event Number | Begin | End | Recombinant Sequence(s) | Minor Parental Sequence(s) | Major Parental Sequence(s) | ORF | RDP | GENECONV | Bootscan | Maxchi | Chimera | SiSscan | 3Seq |
1 | 134,852 | 139,255 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV143-LSDV145 | 5.73E-65 | 5.84E-64 | 1.98E-47 | 6.88E-26 | 7.81E-22 | 3.41E-27 | 1.51E-13 |
2 | 1716 | 4457 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV003-LSDV007 | 1.58E-20 | 4.97E-21 | 4.78E-14 | 3.69E-11 | 1.13E-11 | 1.54E-06 | NS |
3 | 120,400 | 122,490* | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV133-LSDV134 | 1.85E-14 | 1.72E-12 | 4.92E-07 | 5.17E-10 | 5.16E-10 | 7.12E-05 | 5.61E-09 |
4 | 95,204 | 99,293 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV101-LSDV104 | 2.50E-14 | 1.34E-14 | 1.90E-07 | 2.75E-07 | 2.73E-07 | NS | 2.04E-10 |
5 | 139,877* | 144,009 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV146-LSDV149 | 1.80E-13 | 2.34E-09 | 6.64E-04 | 4.45E-12 | 4.42E-12 | NS | 8.06E-11 |
6 | 19,712 | 23,339 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV027-LSDV031 | 5.57E-11 | 3.83E-11 | 1.25E-10 | 2.45E-03 | 2.44E-03 | 2.75E-02 | 1.15E-07 |
7 | 91,356 | 92,836 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV098 | 6.75E-11 | 1.04E-09 | 2.17E-09 | 1.86E-05 | 9.93E-06 | NS | NS |
8 | 85,665 | 89,204 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV091-LSDV094 | 7.73E-12 | 1.18E-08 | 2.68E-03 | 1.25E-05 | 1.05E-05 | NS | 4.55E-07 |
9 | 7070 | 9986 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV011-LSDV014 | 9.63E-12 | 3.19E-09 | 1.10E-06 | 5.44E-07 | 9.18E-07 | NS | 2.84E-07 |
10 | 48,555 | 53,550 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV054-LSDV060 | 1.19E-13 | 4.16E-07 | 5.78E-05 | 2.49E-04 | 1.19E-06 | NS | 7.56E-11 |
11 | 33,932 | 35,060 | LSDV_Indonesia_2022_S1/S4 | AF325528.1_LSDV_NI-2490 | AF409138.1_LSDV_Neethling_vac_1959 | LSDV039 | 4.75E-09 | 3.39E-08 | 8.10E-06 | NS | 1.10E-02 | NS | 6.24E-04 |