Table 3.
Summary of the Reads Mapping of Small RNAs and Transcriptomes by RNA Sequencing
| Rice variety |
Small RNAs |
Transcriptome |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Tissue | Subspecies | Accession Name | Accession No.a | No. of Sequences Generated | No. of Sequences Matching the Rice Genome | No. of Unique Sequences | No. of Sequences Generatedb | No. of Sequences Matching the Rice Genomec | Unique Mapped Readsc |
| Seedling | Indica | Khao Dawk Mali 105 | IRGC 27748 | 9,985,373 | 9,758,028 (97.7%) | 2,786,744 (27.9%) | 20,326,850 | 34,063,783 (83.79%) | 33,569,936 (82.6%) |
| Guangluai 4 | IRGC 114900 | 9,788,880 | 9,558,792 (97.7%) | 3,048,520 (31.1%) | 20,216,686 | 32,972,884 (81.54%) | 32,494,623 (80.4%) | ||
| Rathuwee | IRGC 8952 | 9,997,943 | 9,701,803 (97.0%) | 3,403,862 (34.0%) | 19,876,912 | 32,789,681 (82.48%) | 32,328,952 (81.3%) | ||
| Japonica | Taipei 309 | IRGC 42576 | 8,221,032 | 8,051,214 (97.9%) | 2,282,686 (27.8%) | 19,094,551 | 33,286,973 (87.16%) | 32,855, 807 (86.0%) | |
| Heukgyeong | IRGC 55530 | 9,371,607 | 8,988,554 (95.9%) | 2,203,943 (23.5%) | 19,889,198 | 34,863,682 (87.64%) | 34,372,869 (86.4%) | ||
| Nipponbare | IRGC 12731 | 10,592,461 | 10,416,128 (98.3%) | 3,010,461 (28.4%) | 18,818,192 | 32,995,013 (87.67%) | 32,592,2 62 (86.6%) | ||
| Grain | Indica | Khao Dawk Mali 105 | IRGC 27748 | 14,396,308 | 13,994,396 (97.2%) | 5,408,929 (37.6%) | NA | NA | NA |
| Guangluai 4 | IRGC 114900 | 14,433,295 | 14,137,205 (98.0%) | 4,056,622 (28.1%) | NA | NA | NA | ||
| Rathuwee | IRGC 8952 | 15,718,282 | 15,185,127 (96.6%) | 5,740,388 (36.5%) | NA | NA | NA | ||
| Japonica | Taipei 309 | IRGC 42576 | 14,846,530 | 14,293,090 (96.3%) | 2,786,744 (18.8%) | NA | NA | NA | |
| Heukgyeong | IRGC 55530 | 10,225,740 | 9,512,313 (93.0%) | 3,081,796 (30.1%) | NA | NA | NA | ||
| Nipponbare | IRGC 12731 | 13,862,947 | 13,356,435 (96.4%) | 5,014,395 (36.2%) | NA | NA | NA | ||
| Total | 141,440,398 | 136,953,085 (96.8%) | 42,825,090 (30.3%) | NA | NA | NA | |||
aInternational Rice Germplasm Collection at IRRI in the Philippines (http://archive.irri.org/GRC/requests/requests.htm).
bNumber of pairs of 75-nt paired-ends sequencing reads.
cThe proportion was calculated as the number of mapped reads versus the number of total reads.
NA, Not applicable.