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Table 1 Comparison of whole genome sequencing of Oryza sativa subspecies

From: Indica rice genome assembly, annotation and mining of blast disease resistance genes

Details

HR-12 (current study)

93–11 [2]

IR-64 [3]

Kasalath [4]

Nipponbare [1]

Subspecies

indica

indica

indica

aus

japonica

Sequence depth

73x (Illumina) and 20x (PacBio)

4.2x (Sanger) and 36x (Illumina)

110x (Illumina)

6x (Roche 454) and 148X (Illumina)

6x (Sanger), 62x (Illumina) and 2.57x (Roche 454)

Sequencing technologies

Illumina and PacBio

Sanger and Illumina

Illumina

Illumina and Roche 454

Sanger, Illumina and Roche 454

Genome assembler(s)

MaSuRCA and PBJelly

RePS and SOAPDenovo

ALLPATHS-LG

Celera Assembler and String Graph Assembler

TIGR Assembler

Genome size (Mb)

389.77 (389.60)

374.55 (359.41)

345.9 (321.2)

401.14 (328.25)

374.47 (374.31)

No. of N's (Mb)

0.17

15.14

24.7

72.89

0.17

Total no. of contigs/scaffolds

59,692

50,231

26,160

51,550

NA

a. Anchored contigs/scaffolds

43,781

35,415

NA

36,932

NA

b. Unanchored contigs/scaffolds

15,911

14,816

NA

14,618

NA

N50 (Kb)

28.5

6.69

22.2

13.73

NA

No. of genes

56,284

40,464

37,758

53,662

55,986

CEG mapping (%)

94.35

95.97

94.35

95.97

95.97

  1. Value in parenthesis indicate genome size without ‘N’ content
  2. NA Not available, No. Number, Mb Mega bases, Kb Kilo bases
  3. N50 50 % of the contigs represent this contig length
  4. CEG Core Eukaryotic Genes