Table 1 Polymerase chain reaction (PCR) primer sequences, amplicon lengths and final PCR primer concentrations used in the study.
SNP | Primer (5' - 3') |  | Fragment size (mers) | Concentration (μM) | Assay |
|---|---|---|---|---|---|
| Â | Forward | Reverse | Â | Â | Â |
M170 | CTAGTATGCTTCACACAAATGCG | GACCACACAAAAACAGGTCCTC | 390 | 0.08 | YSNP1 |
M207 | AAGGGCAAGCAAAATAGCAATAC | TGTTCGCTGCTACGAATCTTT | 363 | 0.08 | Â |
M201 | CATGGGTAATTCGGTTGTTACC | CTAAACATCATGGTGTGACGAAC | 331 | 0.08 | Â |
M168 | GGTTTGAATGAGACTGGGTCA | TGGTAATCTCATAGGTCTCTGACTG | 295 | 0.08 | Â |
M343 | AGGTAGGAGGATCCAAAGCTGA | CACCTTTGTCCTCTTGCTCTTT | 276 | 0.08 | Â |
M9 | TGCAGCATATAAAACTTTCAGGAC | TTCCTCATTTTTGAAGCTCGTG | 241 | 0.08 | Â |
M69 | TCAGCCATTTCACCAAAACTCT | CTGAAGAAACAAACCTACCTGGAA | 233 | 0.08 | Â |
M89 | CCAAGCTGGTGAGTCTTATCCT | GCAGAATAGCTGCTCAGGTACA | 215 | 0.08 | Â |
M172 | CAGAAGATGCCCCATTATATCCT | ACTCCATGTTGGTTTGGAACAG | 208 | 0.08 | Â |
M198 | TAGGCACTTGGGAACTTACACTC | TTCTTGTGATAGCATGCCGTTT | 178 | 0.08 | Â |
SRY10831 | CATCCAGTCCTTAGCAACCATT | AATGACACAAGGCACCACATAG | 163 | 0.08 | Â |
P28 | TTTTGAGAGAAGACAAGGGGGATA | TTGGAGGGACATTATTCTCCTGA | 559 | 0.20 | Hg-A |
M13-M14* | ATCACGCCCCTCTCATTGTC | AGCTCTAGATAAAAGCACATTGACACC | 457 | 0.08 | Â |
M91 | GATCACAAAGACCTGGACAGATTACA | AACGGAAATGCCAAGAATCGTA | 429 | 0.05 | Â |
M31 | GCTGAAACAATAGTTCTTCACAATGG | CAGTCCTATGCATAATGCCGTGT | 400 | 0.03 | Â |
M114 | GCCTTGATTTTCTTCGTACTTCATAAG | CCAGTTTCTCACTGAGTTCATTCCTT | 370 | 0.06 | Â |
M28 | GGGCTTCAGTTCTTGACGCTAC | CCGTCTTAATTTTGCGGTATTCAA | 329 | 0.04 | Â |
M51 | AAACCACACCTGTCTTACCAGAGC | CTGTTCCCCAGTTTTCAATCTCC | 293 | 0.04 | Â |
M171 | GGCTGTGTGGAGTATGTGTTGG | CAAATATCCTGCCCCAGCTTAGT | 217 | 0.04 | Â |
M118 | TCCCTTGAAATTAAGGACAACAACT | CATTCTTCTCAACCAGCTGACACT | 167 | 0.06 | Â |
M43 | GACTCCATAAGCAAAAGGTCATCAA | AAAAGAAGTTGAGGACTGGAGCA | 518 | 0.12 | Hg-B |
M112 | GGCCATGCTAACAGAGATCTGAC | CACAGTTCAATTCTTGTCTGTTGC | 493 | 0.08 | Â |
M152 | AAGCAAAAAGCTCCTTCTGAGGT | CAGAAGGTGGATCAGGGTAGAAA | 381 | 0.08 | Â |
M182 | CATTTTTGTGTCAGGTATCCTTTGT | CAAGACGGCGTATCAACTCAAG | 368 | 0.12 | Â |
M108 | GCTTTTCTAACACCACCCATGAC | TATGTGATAGAGGTGGCTTTAAGTGG | 342 | 0.08 | Â |
M150 | CCAGGCTAGCAGTGGAGATGAA | AGGGTGGACTGCTGACCTACTTT | 312 | 0.08 | Â |
M146 | TTACAGGTGGAATGGGGTGTTAC | GAGAAGAACTGCCTTCCATGACATA | 279 | 0.08 | Â |
M60 | CCTGATGTGGACTCAACCTTGTA | TGTTCATTATGGTTCAGGAGGAG | 250 | 0.08 | Â |
M211 | CACTGCACACACTACACTGACCAC | ATGTTGATTGGGTAGAGCCCTTT | 386 | 0.06 | Hg-B2b |
P6 | TATTAGGGAAATCACTCAGGATGGT | TCTACGAATGTTTAACCTCAGATACCG | 343 | 0.12 | Â |
P8 | AGTTGTTGGAAAGCCTCTGTTCA | TGATACTAGACGTGGCATCTTGTCA | 313 | 0.06 | Â |
M115 | TGCCATGCTTGTTTCTTAATCCA | AACTATGTTGCACATCAGCCTCA | 270 | 0.12 | Â |
P7 | GGCCAAAGCCTAGAATGAAATTG | AAGTGCTTGTCCAAGGCAGTATAA | 228 | 0.16 | Â |
M30 | ACAAATCATGAGCTTACAGAACCTG | GGCACAGCCAGATAACCCTACA | 200 | 0.12 | Â |
M40-M41* | TAGCTGGTATGACAGGGGATGAT | GGGTAGGATAGGCTAGCTATTACGC | 435 | 0.08 | Hg-E |
M2 | GGAGAAGAACGGAAGGAGTTCTAA | ACTTGCCAGAGACTTCCAGTTTG | 372 | 0.12 | Â |
M85†| GAACTGGCATCCAATACTAGCTGA | TCACCTCTTTTGTATTGGCTTCTTC | 350 | 0.08 |  |
P2 | TGGTCTGGTAACACCCATAAAGGT | GCAGTTTTCTCAGATGCTTCTCCTA | 335 | 0.08 | Â |
M35 | GCCTAAAGAGCAGTCAGAGTAGAATG | GAGAATGAATAGGCATGGGTTCA | 303 | 0.08 | Â |
M75 | GTCACATTCCACACATCAAGAAAACT | GTGAATCTCTGCCCAGAAAAGAAAA | 274 | 0.12 | Â |
M44 | ATTGGATATGGAAGCCAGTCTCA | ATGTGTTTGAGGACCACCCTAGA | 250 | 0.12 | Â |
M33 | GGCTTCTGTTCAATTTTCCTTTGAT | TTATTTGTTGAAGCCCCCAAGAG | 223 | 0.08 | Â |
M10 | GTTCAAGACAATGAAGGGAGAGACT | TGACATTGACCTGCAGCATAGG | 520 | 0.08 | Hg-E1b1ba |
M191 | GAGCAAGTACAGCGAGCAGTAAG | GGTTTAACACAATGCAGGTCAATTC | 480 | 0.08 | Â |
M154†| CAATGGAGGCTATAGGTGATTGC | CTGTTTGTTCATGGAGATGTCTGTA | 461 | 0.08 |  |
M149†| GAACTGGCATCCAATACTAGCTGA | TCACCTCTTTTGTATTGGCTTCTTC | 350 | 0.06 |  |
M116 | TATGAAGTACGAAGAAAATCAAGGCTA | TGGGTAGAAAAACTGCAAGTAGATGA | 328 | 0.12 | Â |
M58-M155* | TGGGCCTGACCTCTTAACTTGTA | CATAATAAGCTAAGAAACATCCAGCCT | 293 | 0.06 | Â |
M81†| CAATGGAGGCTATAGGTGATTGC | CTGTTTGTTCATGGAGATGTCTGTA | 461 | 0.10 | Hg-E1b1b1 |
M123-M281* | CTAATTCATGCTCTCAGGGGAAA | ATAACCTCTGGAAGTGTGTCTTTACCT | 404 | 0.10 | Â |
M107 | AATCCCACCTCACATACACATAAGC | AGGGGTTGACAAGAAAAAGGAATA | 386 | 0.06 | Â |
M148†| GAACTGGCATCCAATACTAGCTGA | TCACCTCTTTTGTATTGGCTTCTTC | 350 | 0.08 |  |
M78 | ATGGCTGTATGGGTTTCTTTGACT | CGGAATATGGACAGTCATCGTATT | 330 | 0.08 | Â |
M165 | CAAGTCAGCAAGGAGTAGGTGGA | TTGCACTGACACAAGTTATCTCCCT | 293 | 0.08 | Â |
M34 | GATAACCTCATTGTGGAGAGCACTT | ATGCTAAAGCAAGTAACCCTGTGG | 254 | 0.10 | Â |
M136 | ACCAACCGTATTACCTTCTCCTCA | CATGAGTCCAAAGTATAGTGGGCTA | 226 | 0.10 | Â |