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 |