| canSNP name | Target lineage | Position* | Forward Primer (5' - 3') | Reverse Primer (5' - 3') | SNP | Reference |
| A.Br.001 | A.Br.Ames | 182106 | CAAGCGGAACCAAAT TTAATCTTT | TTCACCGTACGTCATTG TATAATACG | T/C | |
| A.Br.002 | A.Br.Ames, A.Br.001/002 | 947760 | AACGATACCTAAAAT CGATAAAG | GGCAGAAGGAGCAAGT AATGTT | G/A | |
| A01 | A.Br.Ames, A.Br.01 | 515111 | CGTGGCGTAAAAATA AAGATCC | TCGTTTGCTGCAACATA ATTTC | A/G | [11] ; this study |
| A02 | A.Br.02 | 240050 | AGCTGCTGAAAATGA TGTAGCA | GAACCATCCCAAAGTTT GATTG | T/C | [11] ; this study |
| Ba20 | A.Br.02 (Fr-Doubs) | 3434997 | AGCGAGCCAATTTTG GAACCGA | AGGCGGGATTGTTGGTG GATGT | A/C | |
| A.Br.003 | A.Br.Ames, A.Br.001/002, A.Br.Aust94 | 1493157 | GCTACTGTCATTGTAT AAAAACCTCCTTT | CGCTTGCCAAGCTTTTTT TC | A/G | |
| A94 | A.Br.Aust94 | 569295 | CCCTGCACCTAACATA ACAACA | CCGCAATGTACCCACTGT ATAA | C/T | [11] ; this study |
| A.Br.004 | A.Br.Ames, A.Br.001/002, A.Br.Aust94, A.Br.003/004 | 3600659 | CCGATACCAGTAAAC GACGACAT | CTGGAATTGGTGGAGCTA TGGA | T/C | |
| A03 | A.Br.003/004 | 3956945 | CGAAAGAACATATTG CACTCGTAA | GCGTACAAGTACAGGCTC ACCT | A/G | this study |
| A05 | A.Br.005/006 | 405303 | CTATATTTTGGACTTG TGCGACAG | GCAATGTTTTGGGAGCTT AGTG | C/T | this study |
| A.Br.006 | A-Clade | 162509 | CCGGAAATTGCTATTA GAACGAA | TCCCAATCTAGCGTTTTTA AGTTCA | C/A | |
| A.Br.007 | A.Br.Vollum | 266439 | TTGGTAACGAGACGAT AAACTGAATAA | GCCTTGGATTGGCGATTG | T/C | |
| A.Br.008 | A.Br.008/009 | 3947248 | TTCGCAACTACGCTATA CGTTTTAGAT | CAAACGGTGAAAAAGTT ACAAATATACG | T/G | |
| A.Br.009 | A.Br.WNA | 2589823 | GGCAATCGGCCACTGT TT | GGGTTTCTACTGTGTATG TTGTTAATAAAAAG | A/G | |
| A.Br.011 | A.Br.011/009 | 2552486 | CTAAAAAGAAACGAAT TCCCGCTGA | CGATAAAAATCGGAATT GAAGCAGGAG | G/A | |
| A11/1 (Ba21) | A.Br.011/009 (Branch 1 Fr) | 3562427 | AGCAAAAAGTCGGCAA AGAA | ACAGAGCTTCCTCCGAA CTG | A/C | |
| A11/2 (Ba22) | A.Br.011/009 (Branch 2 Fr) | 820195 | AGTGGTGCAATCCCAA TTTC | CGCAGCAATATTCGCTA TCA | T/C | |
| A11/3 | A.Br.011/009 (Branch 3) | 1975689 | CACATTGTCAATATTA AATCGCTGA | TGCTTCTCCACCTAAATC AAATG | G/A | this study |
| A11/4 | A.Br.011/009 (Branch 4) | 2571863 | TCCTACACCTGTTTCAC CACAA | AAGCTTGTATCACCAACT GATGC | C/T | this study |
| A11/5 | A.Br.011/009 (Branch 5) | 5021456 | TATTTGTTGAAAGAGC GTCATCC | TGTGTCAGTCTCCGCATA CAATA | T/C | this study |
| A11/6 | A.Br.011/009 (Branch 6) | 1391599 | ACCAAGTAATTAAGTT CCAAGCTATTG | ATTCGCCTTACAAAATGG TTCTC | C/T | this study |
| B.Br.001 | B.Br.KrugerB | 1455279 | TGCATGCTTCTTCTTAC AGAGTAGTTAAT | CGGTCATAAAAGAAATCG GTACAA | T/C | |
| B.Br.002 | B.Br.KrugerB, B.Br.001/002 | 1056740 | TGTTGCACCTTCTGTGT TCGTT | GTAGTGGCTTCACCGAATG GA | G/T | |
| B.Br.003 | B-Clade | 1494269 | CATTTATTCGCATAGAA GCAGATGA | TGTGCCATCAAATAACTCT TTCTCAA | G/A | |
| B.Br.004 | B.Br.CNEVA | 69952 | GAAGTTAAGTATCAACC AGCAGAAGAAA | CCGCCGCCTTGAGCTT | T/C | |
| Ba 19 | B.Br.CNEVA (France) | 2573536 | CATATATTTTCACCTCTT TTATGAACA | GATAAAAGGCTGTCGGATGG | A/G | |
| A/B.Br.001 | C.Br.A1055 | 3697886 | GAAGGTCTCCAATTTGG ATTTAAAAT | CGTGTGAACCTTTCGGTAA ATAGTC | A/G |