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. 2014 Oct 28;14:287. doi: 10.1186/s12870-014-0287-2

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).