Table 2.

Distribution of the SNP effect per type of effect in the four cherry-type ( S. l. cera ) and four S. lycopersicum (S. lyc) lines

		S. l. cera	S. l. cera	S. l. cera	S. l. cera	S. lyc	S. lyc	S. lyc	S. lyc
Accession		Cervil	Plovdiv	LA 1420	Criollo	Stupicke	Ferum	Levovil	LA 0147
High effect	Total	937	701	648	572	273	240	220	184
	Splice site acceptor	109	68	63	50	27	23	25	19
	Splice site donor	104	70	57	64	18	27	17	14
	Stop gained	409	328	294	244	106	76	69	65
	Stop lost	214	169	170	156	86	81	82	65
	Start lost	101	66	64	58	36	33	27	21
Moderate effect	Total	25,632	18,390	14,333	15,713	6,678	5,504	5,915	4,101
Non synonymous coding
Low effect	Total	19,681	13,698	9,700	12,244	4,750	3,624	4,304	2,537
	Non synonymous start	18	13	6	17	4	4	6	4
	Start gained	388	198	183	263	80	39	77	40
	Synonymous coding	19,218	13,448	9,481	11,924	4,654	3,564	4,208	2,485
	Synonymous stop	57	39	30	40	12	17	13	8
Modifier	Total	2,349,654	1,669,629	1,516,290	1,231,706	439,151	366,977	323,588	233,987
	Downstream	395,731	269,917	214,303	226,489	92,087	70,696	63,259	54,897
	Intergenic	1,377,524	1,019,498	1,000,788	676,540	215,862	200,063	164,291	102,012
	Intragenic	26,634	14,937	10,911	15,335	4,212	2,974	5,292	2,319
	Intron	118,329	79,698	60,972	73,234	27,095	20,573	25,094	14,524
	Upstream	422,540	280,576	225,411	234,350	95,053	71,642	63,800	59,194
	UTR 5 Prime	2,540	1,371	1,110	1,551	507	280	1,383	305
	UTR 3 Prime	6,347	3,632	2,795	4,207	1,335	749	469	736

SNPs were annotated using SNPeff onto the SL2.40 reference genome.