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Table 2 Statistics of alignment of four Sultanina de novo assemblies with V. vinifera (PN40024 12X.v2) reference genome

From: Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

 

AP

PLAT_d

MERGE

PLAT*_GC

Total Scaffold number > 1 kbp

17,920

24,112

22,566

23,981

Top-hits-length (95% identity and minimum 1kbp alignment lengtha

99,297,844

131,213,373

126,718,587

152,634,079

Number of scaffolds aligned (95% identity and minimum 1 kbp alignment, % total scaffolds)

10,892 (61%)

16,462 (68%)

15,193 (67%)

16,572 (69%)

Top-hits-length (100% identity and minimum 1 kbp alignment length

470,236

1,824,500

1,604,407

1,509,723

Number of scaffolds aligned, (100% identity and minimum 1 kbp alignment)

187

615

560

558

SyMAP synteny blocks (anchors having alignment lengths >10 kb)b

12,112

13,448

13,421

13,412

  1. aOne-to-one relationship between scaffolds for each assembly and the reference genome were constructed according to the longest alignment for each scaffold, and the total of the alignment lengths (top-hits-length) were calculated
  2. bCalculated with SyMAP [42] used to map with the V. vinifera reference genome