Table 5 Summary of the variants identified in the four S. pimpinellifolium and four S. lycopersicum var. cerasiforme accessions using using Heinz 1706 SL4.0 as a reference genome²⁶ (RF).

From: Morphoagronomic characterization and whole-genome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interspecific tomato MAGIC population

	S. pimpinellifolium										S. lycopersicum var. cerasiforme										Total
	SP1		SP2		SP3		SP4		Mean		SLC1		SLC2		SLC3		SLC4		Mean		Total
	Count	%	Count	%	Count	%	Count	%	Mean	%	Count	%	Count	%	Count	%	Count	%	Count	%	Count	%
Variants
Homozygous SNPs	3,223,730	69.5	3,032,979	78.5	3,879,974	79.4	2,453,673	76.9	3,147,589	76.1	1,497,288	76.0	855,877	68.9	912,198	69.3	1,115,582	72.2	1,095,236	71.6	9,106,964	86.2
Heterozygous SNPs	647,201	14.0	184,801	4.8	209,810	4.3	189,876	6.0	307,922	7.3	129,834	6.6	125,920	10.1	143,599	10.9	149,794	9.7	137,287	9.3	9,106,964	86.2
Homozygous InDels	379,109	8.2	381,565	9.9	447,678	9.2	324,948	10.2	383,325	9.4	217,208	11.1	172,779	13.9	161,126	12.2	175,312	11.3	181,606	12.1	812,034	7.7
Heterozygous InDels	84,534	1.8	18,288	0.4	20,876	0.4	16,667	0.5	35,091	0.8	11,262	0.6	9,928	0.8	9,689	0.7	10,972	0.7	10,463	0.7	812,034	7.7
Homozygous complex	209,751	4.5	188,390	4.8	258,072	5.3	151,032	4.8	201,811	4.9	76,890	3.9	53,003	4.2	60,497	4.6	61,577	4.0	62,992	4.2	579,456	5.5
Heterozygous complex	57,559	1.2	26,997	0.7	32,071	0.6	24,840	0.8	35,367	0.8	18,838	0.9	15,018	1.2	18,388	1.4	18,824	1.2	17,767	1.2	579,456	5.5
Homozygous MNP	32,803	0.7	29,863	0.8	36,797	0.7	23,648	0.7	30,778	0.7	15,916	0.8	9,748	0.8	11,157	0.8	12,513	0.8	12,334	0.8	58,804	0.6
Heterozygous MNP	4906	0.1	2144	0.1	2469	0.1	1937	0.1	2864	0.1	1501	0.1	1,055	0.1	1,261	0.1	1,355	0.1	1,293	0.1	58,804	0.6
Total homozygous	3,845,393	82.9	3,632,797	94.0	4,622,521	94.6	2,953,301	92.7	3,763,503	91.1	1,807,302	91.8	1,091,407	87.8	1,144,978	86.9	1,364,984	88.3	1,352,168	88.7	–	–
Total heterozygous	794,200	17.1	232,230	6.0	265,226	5.4	233,320	7.3	381,244	9.0	161,435	8.2	151,921	12.2	172,937	13.1	180,945	11.7	166,810	11.3	–	–
Total variants	4,639,593	100.0	3,865,027	100	4,887,747	100.0	3,186,621	100.0	4,144,747	100.0	1,968,737	100.0	1,243,328	100.0	1,317,915	100.0	1,545,929	100.0	1,518,977	100.0	10,557,258	100.0
% het. variants with RF	0.103		0.030		0.034		0.030		0.049		0.021		0.020		0.022		0.023		0.022
% total variants with RF	0.600		0.500		0.632		0.412		0.536		0.255		0.161		0.171		0.200		0.197
Private variants	771,181	16.6	748,354	19.3	1,115,616	22.8	985,453	30.9	905,151	22.4	339,481	17.2	467,864	37.6	190,559	14.5	279,295	18.0	319,299.8	21.8	4,897,803	46.3
Variants in coding regions
Homozygous SNPs	307,824	58.6	321,285	71.8	375,090	72.3	253,723	69.1	314,481	68.0	124,716	65.0	92,841	60.0	78,951	56.0	80,019	55.2	94,132	59.1	996,772	82.4
Heterozygous SNPs	107,212	20.4	30,776	6.9	32,981	6.4	34,522	9.4	51,373	10.8	22,275	11.6	23,504	15.2	27,654	19.6	30,294	20.9	25,932	16.8	996,772	82.4
Homozygous InDels	58,463	11.1	61,945	13.9	70,754	13.7	51,374	14.0	60,634	13.2	29,821	15.6	26,057	16.9	22,305	15.8	22,568	15.5	25,188	15.9	131,056	10.8
Heterozygous InDels	16,675	3.2	3073	0.7	3411	0.6	2899	0.8	6515	1.3	1802	0.9	1,719	1.1	1,612	1.1	1,880	1.3	1,753	1.1	131,056	10.8
Homozygous complex	22,053	4.2	22,772	5.0	27,306	5.3	17,461	4.8	22,398	4.8	8323	4.3	6,548	4.2	5,826	4.1	5,476	3.8	6,543	4.1	76,511	6.3
Heterozygous complex	10,199	1.9	4550	1.0	5509	1.0	4551	1.2	6202	1.3	3326	1.7	2,864	1.9	3,763	2.7	3,835	2.6	3,447	2.2	76,511	6.3
Homozygous MNP	2831	0.5	2816	0.6	3228	0.6	2206	0.6	2770	0.6	1282	0.7	947	0.6	849	0.6	872	0.6	988	0.6	5,909	0.5
Heterozygous MNP	749	0.1	327	0.1	342	0.1	315	0.1	433	0.1	220	0.1	170	0.1	212	0.1	203	0.1	201	0.1	5,909	0.5
Total homozygous	391,171	74.3	408,818	91.3	476,378	91.8	324,764	88.5	400,283	86.5	164,142	85.6	126,393	81.7	107,931	76.4	108,935	75.0	126,850	79.7	–	–
Total heterozygous	134,835	25.7	38,726	8.7	42,243	8.2	42,287	11.5	64,523	13.5	27,623	14.4	28,257	18.3	33,241	23.6	36,212	25.0	31,333	20.3	–	–
Total variants	526,006	100.0	447,544	100.0	518,621	100.0	367,051	100.0	464,806	100.0	191,765	100.0	154,650	100.0	141,172	100.0	145,147	100.0	158,184	100.0	1,210,248	100.0
% het. variants with RF	0.017		0.005		0.005		0.005		0.008		0.003		0.004		0.004		0.005		0.004
% variants with RF	0.068		0.058		0.067		0.047		0.060		0.024		0.020		0.018		0.019		0.020

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Table 5 Summary of the variants identified in the four S. pimpinellifolium and four S. lycopersicum var. cerasiforme accessions using using Heinz 1706 SL4.0 as a reference genome²⁶ (RF).

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