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Table 4 Number of polymorphisms in the upland NERICA

From: Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Genotype Category Allele type CG 14 allele (%) Non-parental allele (%)
WAB56–104 CG 14 Non-parental Category All Category All
NERICA 1 SNP 2464390 247641 101458 8.80 9.03 3.61 3.81
MNP 79607 6336 8975 6.68 9.46
Short InDel 324348 43036 14852 11.26 3.89
NERICA 2 SNP 1485308 148296 42301 8.85 8.68 2.52 2.65
MNP 46795 3990 3566 7.34 6.56
Short InDel 171010 14367 5123 7.54 2.69
NERICA 3 SNP 2989656 41101 39623 1.34 1.32 1.29 1.39
MNP 98929 671 3991 0.65 3.85
Short InDel 333122 4601 5371 1.34 1.57
NERICA 4 SNP 3008891 41574 40255 1.35 1.33 1.30 1.41
MNP 99336 681 4059 0.65 3.90
Short InDel 322610 4520 5457 1.36 1.64
NERICA 5 SNP 2637694 293878 79951 9.76 9.81 2.65 2.91
MNP 85743 8884 7838 8.67 7.65
Short InDel 275398 34231 12349 10.63 3.84
NERICA 7 SNP 2471034 117058 82482 4.38 4.32 3.09 3.36
MNP 74904 1816 8946 2.12 10.44
Short InDel 272139 12842 11127 4.34 3.76
NERICA 8 SNP 1476391 98444 96093 5.89 5.82 5.75 6.05
MNP 46196 1787 8550 3.16 15.12
Short InDel 164605 11231 11142 6.01 5.96
NERICA 9 SNP 1786210 120441 116935 5.95 5.88 5.78 6.10
MNP 54940 2150 10599 3.18 15.66
Short InDel 203351 13928 14197 6.02 6.13