Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

BMC Genomics

Table 3 Number of common SNP (upper diagonal) and InDel (lower diagonal) in all the pairs of comparisons (SNP defined with a depth higher than 4 in both accessions, except for LA 1589, S. pimpinellifollium )

		S. lyc	S. lyc	S. lyc	S. lyc	S. l. cera	S. l. cera	S. l. cera	S. l. cera	S. pim
SNP InDel	Nb vs Ref.	LA0147	Levovil	Ferum	Stupicke	Criollo	LA1420	Plovdiv	Cervil	LA 1589
Nb vs Ref.		182,371	271,458	306,083	356,655	1,042,928	1,358,257	1,457,098	2,028,568	4,524,892
LA 0147	7,969		82,460	85,695	116,904	63,915	79,616	76,642	87,389	76,628
Levovil	2,894	517		49,318	80,009	54,538	49,482	53,472	78,907	67,886
Ferum	4,532	715	353		71,995	122,094	116,987	68,448	64,689	207,309
Stupicke	10,886	1,544	540	738		70,024	217,565	244,284	111,531	193,353
Criollo	13,898	612	336	601	727		458,908	164,449	260,234	501,982
LA 1420	30,927	1,298	468	910	2,366	2,666		310,635	222,517	537,839
Plovdiv	33,966	1,227	460	722	2,621	1,262	3,106		828,296	1,065,584
Cervil	53,522	1,521	534	807	1,746	1,811	2,532	8,441		1,538,643
LA 1589	201,502	304	771	328	591	910	1,519	3,273	5,707

Accessions consist in four S. lycopersicum (S. lyc), four cherry-type (S. l. cera) and one S. pimpinellifolium (S. pim) accessions. The first line and column indicate the number of SNP and InDel detected when compared to the reference genome [11].

ISSN: 1471-2164