Table 1.
Comparison results of leaf and root sequences on the reference genome
| Samples | Valid reads | Mapped reads | Multi Mapped reads | Non-splice reads | Splice reads |
|---|---|---|---|---|---|
| AR | 51128076 | 42941674 (84.1%) | 13374298 (26%) | 23022576 (45.1%) | 15385894 (30.1%) |
| AL | 50223934 | 48695890 (96.9%) | 16157539 (32.1%) | 25789688 (51.3%) | 17081456 (34%) |
| BR | 54107099 | 46993196 (86.8%) | 14846539 (27.4%) | 25014416 (46.2%) | 16974977 (31.3%) |
| BL | 49707365 | 48244852 (97.1%) | 16086388 (32.3%) | 25040718 (50.3%) | 17076845 (34.3%) |
| CR | 50767484 | 41842045 (82.4%) | 13216507 (32%) | 22208395 (43.7%) | 15152915 (29.8%) |
| CL | 42235064 | 40631339 (96.2%) | 13500391 (32%) | 21646516 (51.2%) | 13975171 (33.1%) |
| DR | 52834574 | 41081382 (77.7%) | 12835496 (24.3%) | 22221619 (42.1%) | 14574574 (27.6%) |
| DL | 44050304 | 42327643 (96.1%) | 14086443 (32%) | 22479693 (51%) | 14580814 (33.1%) |
| HR | 43141279 | 38301647 (88.8%) | 12126751 (28.1%) | 20191122 (46.8%) | 13615361 (31.1%) |
| HL | 45690950 | 44124014 (96.5%) | 14800421 (32.4%) | 23403306 (51.2%) | 14810568 (32.3%) |
| MR | 46272200 | 39103323 (84.8%) | 12391214 (26.9%) | 20472287 (44.4%) | 14045575 (30.5%) |
| ML | 43028428 | 39441113 (91.8%) | 14204489 (32.9%) | 20481512 (47.7%) | 13220392 (30.8%) |
| LR | 45335083 | 38959747 (85.9%) | 12539366 (27.6%) | 20368492 (44.9%) | 13919944 (30.7%) |
| LL | 45513687 | 42998982 (94.7%) | 14537458 (31.9%) | 22837449 (50.2%) | 14431801 (31.7%) |
In the table, R Root, L leaf, H high, M Medium and L Low. A, B, C, and D represents four inbred parents. Mapped reads represent the number of sequences that were mapped to the reference genome. Multi-mapped reads aligned multiple positions on the referenced sequence. Non-splice reads were those that not showed splicing. Spliced reads represent alternative splicing events