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

Rice

Table 4 Number of polymorphisms in the upland NERICA

Genotype	Category	Allele type			CG 14 allele (%)		Non-parental allele (%)
Genotype	Category	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