Table 3. Summary of single nucleotide polymorphism types identified in three wheat genomes using the wheat Chinese Spring survey sequence (CSSS) assembly.

Allele	1A	2A	3A	4A	5A	6A	7A	A genome	1B	2B	3B	4B	5B	6B	7B	B genome	1D	2D	3D	4D	5D	6D	7D	D genome	NA
No. of SNP	2,151	2,578	1,188	1,647	898	1,926	2,057	12,445	2,464	3,782	4,307	1,519	3,408	1,661	1,517	18,658	906	1,019	348	114	657	911	1,220	5,175	29,282
Density (SNP/Mbp)	2.7	2.87	1.43	1.92	1.09	2.73	2.53	2.17	2.9	4.08	4.34	1.85	3.92	1.82	1.69	2.97	1.5	1.4	0.45	0.18	0.88	1.28	1.68	1.05	-
Transition	1,490	1,830	813	1,113	606	1,326	1,417	8,595	1,707	2,671	2,994	1,026	2,372	1,116	1,049	12,935	568	647	216	92	440	574	796	3,333	20,132
A/G	704	897	371	489	273	591	645	3,970	793	1,214	1,394	472	1,114	527	474	5,988	263	293	88	53	210	262	379	1,548	9,650
C/T	632	732	346	478	277	577	619	3,661	722	1,117	1,219	449	995	472	462	5,436	235	271	93	33	183	251	326	1,392	8,102
T/C	74	104	46	68	19	69	75	455	89	153	169	56	116	59	65	707	36	45	13	4	25	29	46	198	1,140
G/A	80	97	50	78	37	89	78	509	103	187	212	49	147	58	48	804	34	38	22	2	22	32	45	195	1,240
Transversion	661	748	375	534	292	600	640	3,850	757	1,111	1,313	493	1,036	545	468	5,723	338	372	132	22	217	337	424	1,842	9,150
A/T	87	136	50	71	39	90	91	564	106	145	195	76	125	93	58	798	45	57	19	4	33	50	61	269	1,271
A/C	146	199	83	130	56	125	159	898	155	267	313	96	253	131	120	1,335	77	83	33	4	51	77	106	431	2,145
T/A	9	17	9	8	13	8	17	81	15	18	29	10	17	21	9	119	7	7	1	0	1	3	4	23	198
T/G	8	13	8	8	12	17	17	83	20	36	46	19	28	9	18	176	13	9	4	1	6	14	8	55	270
C/A	17	22	8	11	7	21	15	101	21	39	32	10	40	6	16	164	8	12	3	0	8	11	9	51	242
C/G	203	197	127	174	91	193	181	1,166	240	335	368	147	316	151	156	1,713	106	121	38	8	66	98	138	575	2,844
G/T	167	142	76	103	62	126	138	814	165	238	282	118	215	105	74	1,197	68	68	24	5	43	63	80	351	1,778
G/C	24	22	14	29	12	20	22	143	35	33	48	17	42	29	17	221	14	15	10	0	9	21	18	87	402
Ts %	69.27	70.99	68.43	67.58	67.48	68.85	68.89	69.06	69.28	70.62	69.51	67.54	69.60	67.19	69.15	69.33	62.69	63.49	62.07	80.70	66.97	63.01	65.25	64.41	68.75
Tv %	30.73	29.01	31.57	32.42	32.52	31.15	31.11	30.94	30.72	29.38	30.49	32.46	30.40	32.81	30.85	30.67	37.31	36.51	37.93	19.30	33.03	36.99	34.75	35.59	31.25
Ts/Tv ratio	2.25	2.45	2.17	2.08	2.08	2.21	2.21	2.23	2.25	2.40	2.28	2.08	2.29	2.05	2.24	2.26	1.68	1.74	1.64	4.18	2.03	1.70	1.88	1.81	2.20