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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