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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 )

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

   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  
  1. 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].