| Variant ID: vg0227217052 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 27217052 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAATGTGATGAGATCAAGAGGGCTAAATCATTTAGTCGCGGATTCTACAAAGTTATTGTTCTTTTGATCATGGTTTATTTGACGAAAAGAAATATCACGC[A/C]
CCTGCCATTCTTGCACGCCCTGTAAGCTCTCCGGATCGAGCTTCTTGACGGCGACGGCCATGCCGGAGCCGCTCCGCGCGGGGCTCATGGTCCTCTCGTC
GACGAGAGGACCATGAGCCCCGCGCGGAGCGGCTCCGGCATGGCCGTCGCCGTCAAGAAGCTCGATCCGGAGAGCTTACAGGGCGTGCAAGAATGGCAGG[T/G]
GCGTGATATTTCTTTTCGTCAAATAAACCATGATCAAAAGAACAATAACTTTGTAGAATCCGCGACTAAATGATTTAGCCCTCTTGATCTCATCACATTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.50% | 0.10% | 1.67% | 0.68% | NA |
| All Indica | 2759 | 99.50% | 0.10% | 0.07% | 0.33% | NA |
| All Japonica | 1512 | 93.90% | 0.10% | 4.83% | 1.19% | NA |
| Aus | 269 | 98.10% | 0.00% | 0.37% | 1.49% | NA |
| Indica I | 595 | 99.30% | 0.30% | 0.17% | 0.17% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 99.50% | 0.00% | 0.11% | 0.44% | NA |
| Indica Intermediate | 786 | 99.50% | 0.10% | 0.00% | 0.38% | NA |
| Temperate Japonica | 767 | 90.10% | 0.10% | 7.82% | 1.96% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 3.73% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0227217052 | A -> DEL | LOC_Os02g44920.1 | N | splice_donor_variant | Average:76.291; most accessible tissue: Minghui63 flag leaf, score: 83.621 | N | N | N | N |
| vg0227217052 | A -> C | LOC_Os02g44920.1 | splice_donor_variant&intron_variant ; HIGH | splice_donor_variant | Average:76.291; most accessible tissue: Minghui63 flag leaf, score: 83.621 | N | N | N | N |