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Table 1 Summary of the different datasets, chromosomal distribution and physical map length of SNP markers used in the present study

From: Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

Chromosome All SNPs used for genotyping Dataset-1a Dataset-2b Number of SNPs polymorphic within Map length (bp)
O. glaberrima (N = 2358) O. barthii (N = 115) O. glaberrima and O. barthii (N = 2473) Lowland O. sativa (N = 554) Upland O. sativa (N = 218) All O. sativa (N = 772)
Chr1 3124 3113 2758 309 570 390 1636 1046 1796 43,229,577
Chr2 2812 2809 2458 281 468 333 1429 742 1566 35,885,080
Chr3 2678 2668 2333 256 508 326 1362 897 1573 36,413,113
Chr4 2378 2368 2077 242 380 300 1243 845 1376 35,497,590
Chr5 1914 1914 1685 212 378 256 916 565 1024 29,763,242
Chr6 2167 2156 1880 232 437 322 1274 848 1361 31,190,621
Chr7 2017 2011 1793 226 399 282 1016 658 1146 29,679,399
Chr8 1877 1877 1668 148 288 188 1298 723 1336 28,429,363
Chr9 1559 1558 1387 157 267 192 849 389 943 22,947,498
Chr10 1576 1573 1453 225 301 253 788 559 878 23,205,328
Chr11 2085 2085 1851 318 449 352 1233 987 1405 29,000,206
Chr12 1946 1941 1736 234 362 290 1062 601 1170 27,504,691
Unmapped 5606          
Total 31,739 26,073 23,079 2840 4807 3484 14,106 8860 15,574 372,745,708
Polymorphism (%)   82.1 88.5 10.9 18.4 13.4 54.1 34.0 59.7  
  1. aDataset-1 refers to the number of SNPs with two alleles irrespective of minor allele frequency (MAF)
  2. bDataset-2 refers to the number of polymorphic SNPs across all 3245 accessions, each with a minor allele frequency of ≥ 0.01
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