Table 1.

Reference-guided assembly metrics

	Heinz 1706^	LA1589	Gh13	BTI-87	LA1932*
Filtered reads in millions	462.7	281.5	392.9	402.267066
Mapped reads (% mapped)	426.1 (92.1%)	247.7 (88%)	385.4 (98%)	380.9 (94.7%)
Coverage depth	39.3	25	14.7	32.3
Coverage of tomato genome	0.992	0.95	0.976	0.965
Number of gaps (Mb)	76,276 (5.9)	209,919 (38.9)	90,727 (9.2)	165,894 (79.9)
Gaps >500 bp	1,660	14,396	3,058	19,479
Gaps >5000 bp			247	286
SNPs		2,753,307 (0.35%)	288,640 (0.037%)	702,560 (0.09%)	8,123,431 (1%)
Indels		437,943	69,289	130,029	718,185

^Subset of the available libraries for comparison purposes.

*Low coverage reference-based assembly.

LA1589 (S. pimpinellifolium) and LA1932 (S. chilense).