Table 1 A summary of the 25 recombination events detected using the RDP (R), GENECONV (G), BOOTSCAN (B), MAXCHI (M), CHIMAERA (C), SISCAN (S), and 3SEQ (T) methods implemented in the computer program RDP5.
Event | Number of sequences | Recombinant region | Recombinant sequence (s)/genotype | Minor parent sequence (s)/genotype | Major parent sequence (s)/genotype | Detection method | p-value | ||
|---|---|---|---|---|---|---|---|---|---|
Before commune housing | After commune housing | Begin | End | ||||||
1 | 31 | 31 | 1467 | 2038 | BV_1c_C1/IX genotype I except: SI_1a_C4; SI_2a_C1-4; BI2b_C3 | BV_3d_C4/IV | BV_3d_C9/XI | RGBMCST | 3.69 × 10–49 |
2 | 1 | 0 | 1487 | 1958 | SI_1a_C1/III | BI_2b_C6/II | SI_1a_C5/VI | RGMCST | 4.79 × 10–49 |
3# | 0 | 1 | 575 | 1487 | BI_2b_C6/II | BI_2b_C8/II | SI_2a_C3/I; SI_1a_C4 | GBMCT | 1.69 × 10–50 |
4 | 1 | 0 | 378 | 1298 | SI_1a_C5/VI | SI_1a_C1/I | SI_1a_C2/VI | GMCT | 5.95 × 10–33 |
5 | 8 | 189 | 1894 | 614 | genotype XI except: BII_2c_C4 and C8 BV_2a_C1 and C4 BV_2b_C9; BII_1d_C11 | BII_2c_C8/ XI | BII_1d_C11/XI | RGBMCST | 2.50 × 10–30 |
6 | 13 | 197 | 2021 | 179 | Genotype XI except: BV_2b_C9; BII_1d_C11; BV_2a_C4; BII_2c_C4 genotype XIII (all) | Genotype VI except: BIII_3a_C1,C3,C5 and C10 SI_1a_C1/III | BII_1d_C11/XI; BV_2a_C4/XI; BV_2b_C9/XI | RGBMCST | 7.55 × 10–26 |
7# | 0 | 1 | 1441 | 2022 | BV_3d_C4/IV | Genotype I: SI_2a_C1, 3, 4; SI_1a_C4; BI_2b_C3 | BIV_1a_C5/V | RGMCST | 5.87 × 10–49 |
8# | 0 | 1 | 2011 | 99 | BIII_2b_C2/XI | BIII_3a_C5/VI | BII_1d_C11/XI | RGBMCT | 1.05 × 10–21 |
9# | 0 | 1 | 1324 | 1820 | BII_2c_C8/XI | SI_2a_C3/I | BII_1d_C11/XI | RGMST | 1.30 × 10–30 |
10 | 1 | 0 | 1465 | 1622 | BIV_3a_C10/X | BV_2b_C9/XI | BIV_3a_C8/X | GMCST | 1.64 × 10–22 |
11 | 1 | 0 | 1959* | 608 | SI_1a_C1/III | SI_1a_C2/VI | SI_2a_C3/I BI_2b_C3/I | GBMCST | 3.65 × 10–32 |
12 | 7 | 6 | 1195 | 2019 | SI_1a_C1/III Genotype VI except: SI_1a_C5 | Genotype VIII (all) | Genotype XI: BV_2b_C9; BV_2a_C1,C4; BII_2c_C4,C8; BII_1d_C11 | RGBMCST | 1.48 × 10–15 |
13# | 0 | 1 | 73 | 574* | BII_2c_C4/XI | SI_1a_C5/VI | Genotype X (all) | RGMCST | 1.56 × 10–13 |
14 | 1 | 0 | 2021 | 72* | SI_1a_C5/VI | Genotype XII (all) | SII_1c_C2/VIII | RGMCST | 2.97 × 10–12 |
15# | 0 | 2 | 110* | 510 | BIII_2b_C2/XI; BII_1d_C11/XI | BIV_3a_C6/I; BV_1a_C3/I | BII_2c_C4/XI | RGMCST | 1.38 × 10–11 |
16 | 0 | 10 | 1203 | 1913 | Genotype VII (all) | Genotype V (all) | Genotype I: SI_1a_C4; SI_2a_C1,C3,C4; BI_2b_C3 | RGMCST | 2.38 × 10–14 |
17 | 1 | 3 | 2019 | 149 | BV_1c_C1/IX; BV_2b_C9/XI; BV_2a_C4/XI; BII_1d_C11/XI | Genotype I: SI_2a_C1, C3,C4; SI_1a_C4; BI_2b_C3; genotype II (all) | Genotype XII (all) | RGMCST | 7.19 × 10–9 |
18# | 0 | 1 | 1* | 289 | BV_1c_C1/IX | BIV_3a_C6/I | BII_2c_C4/XI | RGMCST | 3.11 × 10–10 |
19 | 36 | 32 | 1* | 137 | genotype II (all); genotype VI (all) | genotype X (all) | BV_3d_C4/IV; BII_3a_C5/VI; genotype V (all) | RGMCST | 5.65 × 10–9 |
20 | 4 | 3 | 1351 | 1897 | Genotype I: SI_2a_C1,C3,C4; SI_1a_C4; BI_2b_C3; genotype II (all) | Genotype V (all) | Genotype XI: BV_2b_C9; BII_1d_C11; BII_2c_C4; BII_2b_C2; BV_2a_C1,C4; genotype XII except BII_3a_C8; SI_3a_C1/XIII; SI_3g_C3/XIII | RGMCST | 2.62 × 10–9 |
21 | 2 | 0 | 2034* | 73 | SI_1a_C2/VI; BIII_3a_C5/VI | BV_3d_C4/IV; genotype V (all) | genotype XI: BII_2c_C4; BII_1d_C11; BV_2a_C4; BV_2b_C9 | RGMCT | 3.80 × 10–7 |
22 | 5 | 2 | 2022 | 72* | Genoptype XII (all) | BIV_1a_C3/V; BIV_2a_C4/V | BII_2c_C4/XI | RGMCT | 1.94 × 10–8 |
23 | 1 | 0 | 192* | 476* | SI_1a_C5/VI | BV_2a_C1/XI; BII_2c_C8/XI | SII_1c_C2/VIII | RGCST | 7.84 × 10–7 |
24 | 8 | 0 | 1915 | 268 | Genotype X (all) | Genotype VIII (all) | Genotype V (all) | RGBMCST | 9.0,3 × 10–7 |
25# | 0 | 1 | 510 | 765 | BV_3c_C9/I | BV_2b_C9/XI; BII_1d_C11/XI | BIV_3a_C6/I | GBMCST | 1.08 × 10–7 |
