| Variant ID: vg0114526630 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526630 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GATTTTCTGTTTAGGGGAAATTTTAGAGTTGTGTTTTTCTGCTAGGGAATAGATGGTTCTCCAAGTTAGCTCTTATTTGTCGGACTGCAGGAATAGTTCT[G/A]
CAAATAAGAAACACATGATCAAAACTAGAAAAGAAGCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTGAAGATTCACCAAATCGAGA
TCTCGATTTGGTGAATCTTCAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGCTTCTTTTCTAGTTTTGATCATGTGTTTCTTATTTG[C/T]
AGAACTATTCCTGCAGTCCGACAAATAAGAGCTAACTTGGAGAACCATCTATTCCCTAGCAGAAAAACACAACTCTAAAATTTCCCCTAAACAGAAAATC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.00% | 0.70% | 0.11% | 4.13% | NA |
| All Indica | 2759 | 91.70% | 1.20% | 0.18% | 6.92% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 95.00% | 0.00% | 0.17% | 4.87% | NA |
| Indica II | 465 | 97.20% | 0.00% | 0.22% | 2.58% | NA |
| Indica III | 913 | 89.00% | 2.50% | 0.11% | 8.32% | NA |
| Indica Intermediate | 786 | 88.90% | 1.40% | 0.25% | 9.41% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526630 | G -> A | LOC_Os01g25630.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:43.417; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |
| vg0114526630 | G -> DEL | N | N | silent_mutation | Average:43.417; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |