Table 1 Reference-guided assembly metrics

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