Table 3.

Heteroplasmic mitochondrial SNPs in the next generation of Col-0 wild-type, UNG mutant lines, Col-0 MTP-A3G, and UNG MTP-A3G: SNPs were called using VarDict as described in the Methods section. SNP counts are shown for the entire mitochondrial genome. For the full spectrum of SNP types, including allele frequencies, see Supplementary File 2.

Sample	A-C	A-G	A-T	C-A	C-G	C-T	G-A	G-C	G-T	T-A	T-C	T-G	Total	GC-AT/Total Ratio
Col-0 1 Young	0	224	3	0	0	4	6	0	0	3	227	0	467	0.0214
Col-0 2 Young	0	45	1	0	0	2	0	0	0	2	33	1	84	0.0238
UNG11 163 1 Young	0	205	4	0	0	7	7	0	0	4	216	0	443	0.0316
UNG11 163 2 Young	1	27	2	0	0	0	1	0	0	0	47	0	78	0.0128
UNG11 176 1 Young	0	65	0	0	0	0	2	0	0	3	79	0	149	0.0134
UNG11 176 2 Young	0	194	0	0	0	2	5	0	0	7	171	0	379	0.0185
UNG11 198 1 Young	1	62	2	0	0	2	1	0	0	1	59	0	128	0.0234
UNG11 198 2 Young	0	63	2	0	0	0	1	0	0	4	68	0	138	0.00725
Col-0 MTP A3G 1 Young	0	151	5	2	0	11	15	0	1	2	158	0	345	0.0754
Col-0 MTP A3G 2 Young	0	154	2	0	0	7	3	0	1	6	136	0	309	0.0324
UNG MTP A3G 1 Young	0	84	0	0	0	3	4	0	0	2	82	0	175	0.04
UNG MTP A3G 2 Young	0	49	2	0	0	2	1	0	0	1	46	2	103	0.0291
Col-0 1 Mature	0	50	0	0	0	3	3	0	0	1	54	0	111	0.0541
Col-0 2 Mature	0	65	2	1	0	2	1	0	0	4	60	0	135	0.0222
UNG11 163 1 Mature	0	1	0	0	0	0	0	0	0	0	3	0	4	0
UNG11 163 2 Mature	0	2	0	0	0	0	0	0	0	0	6	0	8	0
UNG11 176 1 Mature	0	35	2	0	0	2	1	0	0	2	50	1	93	0.0323
UNG11 176 2 Mature	0	50	0	0	0	1	2	0	0	0	57	0	110	0.0273
UNG11 198 1 Mature	0	42	1	0	0	0	2	0	0	1	42	0	88	0.0227
UNG11 198 2 Mature	0	29	2	0	0	1	0	0	0	0	33	0	65	0.0154
Col-0 MTP A3G 1 Mature	0	4	0	0	0	0	1	0	0	0	3	0	8	0.125
Col-0 MTP A3G 2 Mature	0	14	0	0	0	9	12	0	0	0	10	0	45	0.467
UNG MTP A3G 1 Mature	0	13	0	0	0	33	41	0	0	0	13	0	100	0.74
UNG MTP A3G 2 Mature	0	78	1	0	0	25	36	0	1	0	69	0	210	0.290