Table 3 Summary of possible recombination events in SDlz1601, SDhz1512 and SDYG1606 isolates identified by RDP4.
From: Emergence of Different Recombinant Porcine Reproductive and Respiratory Syndrome Viruses, China
Event number | Recombinant Sequence(s) | Breakpoint position(s) | Parental sequence | Recombinant score | P-Value for the six detection methods in RDP4 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
In Recombinant Sequence | Begin/End | Minor/Major | RDP | GENECONV | Bootscan | Maxchi | Chimaera | SiSscan | 3Seq | ||
1 | SDYG1606 | 4823/8190 | JXA1/NADC30 | 0.697 | 7.94E-113 | 8.32E-116 | 5.58E-120 | 1.54E-42 | 4.35E-09 | 1.46E-50 | 2.16E-11 |
2 | SDYG1606 | 1/1818 | SX1/JL580 | 0.685 | 1.88E-152 | 4.56E-131 | 1.21E-136 | 2.56E-35 | 4.50E-34 | NS | 2.16E-11 |
3 | SDYG1606 | 12098/12358 | HNyc15/NADC30 | 0.65 | 7.37E-06 | 1.63E-04 | NS | 2.72E-04 | 2.10E-04 | NS | 2.42E-05 |
4 | SDhz1512 | 9088/11240 | HN1/SX09 | 0.673 | NS | 1.67E-76 | 8.97E-80 | 8.10E-15 | 1.70E-14 | 4.21E-32 | NS |
5 | SDhz1512 | 5732/6302 | SD1100/SX1 | 0.661 | NS | 5.35E-32 | 2.59E-34 | 7.42E-09 | 1.82E-13 | 7.25E-13 | 2.16E-11 |
6 | SDhz1512 | 11241/14635 | NADC30/JXA1 | 0.741 | 5.53E-110 | NS | 5.07E-90 | 9.09E-32 | 2.47E-09 | 4.85E-33 | 2.88E-11 |
7 | SDhz1512 | 7303/8111 | SD1100/JXA1 | 0.67 | NS | 1.85E-31 | 7.03E-35 | 2.17E-11 | 6.16E-12 | 9.15E-13 | 2.16E-11 |
8 | SDhz1512 | 4702/14982 | WUH5/SX1 | 0.624 | 2.02E-14 | 8.23E-08 | 2.46E-18 | NS | NS | NS | 1.44E-11 |
9 | SDhz1512 | 56/365 | VR2332/JXA1 | 0.617 | 2.27E-17 | 2.61E-12 | 2.18E-11 | 7.33E-04 | 2.05E-04 | NS | 6.48E-11 |
SDhz1512 | 1944/2021 | HNjz15/HLJB1 | 0.628 | 7.966E-10 | 3.40E-04 | 5.26E-03 | NS | NS | NS | 0.000249 | |
10 | SDhz1512 | 2062/3163 | SX1/Unknown | 0.429 | 2.03E-12 | 1.48E-20 | 1.09E-08 | 8.42E-07 | 7.58E-07 | 3.29E-13 | 7.20E-12 |
11 | SDlz1601 | 360/2020 | SX1/NADC30 | 0.549 | 4.12E-108 | 3.29E-113 | 1.53E-98 | 7.93E-38 | 1.58E-38 | 1.40E-39 | NS |
12 | SDlz1601 | 3004/7473 | JXA1/NADC30 | 0.629 | 1.36E-75 | 3.48E-87 | 2.41E-83 | 1.48E-44 | 1.77E-10 | 1.90E-64 | 3.78E-08 |
13 | SDlz1601 | 12986/13638 | JXA1/NADC30 | 0.674 | 4.37E-48 | 1.61E-40 | 1.28E-38 | 8.34E-14 | 3.55E-15 | 5.33E-16 | 1.44E-11 |
14 | SDlz1601 | 12057/12662 | TJbd141/NADC30 | 0.663 | NS | 5.92E-37 | 2.25E-44 | 1.01E-14 | 1.72E-12 | 6.58E-18 | 1.44E-11 |
15 | SDlz1601 | 1/354 | NVDCSDXX2013/JL580 | 0.549 | 7.19E-18 | 9.17E-12 | 1.61E-17 | 1.93E-02 | 3.91E-03 | 5.06E-04 | NS |
16 | SDlz1601 | 1944/ 2021 | NADC30/JXA1 | 0.628 | 7.966E-10 | 0.0003397 | 0.0052645 | NS | NS | NS | 0.000249 |
