| Variant ID: vg0114526665 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526665 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTTCTGCTAGGGAATAGATGGTTCTCCAAGTTAGCTCTTATTTGTCGGACTGCAGGAATAGTTCTGCAAATAAGAAACACATGATCAAAACTAGAAAAGA[A/G]
GCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTGAAGATTCACCAAATCGAGAATATGGCATCTCTACCAAATCGACAATATAGCATC
GATGCTATATTGTCGATTTGGTAGAGATGCCATATTCTCGATTTGGTGAATCTTCAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGC[T/C]
TCTTTTCTAGTTTTGATCATGTGTTTCTTATTTGCAGAACTATTCCTGCAGTCCGACAAATAAGAGCTAACTTGGAGAACCATCTATTCCCTAGCAGAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.00% | 0.10% | 0.61% | 4.25% | NA |
| All Indica | 2759 | 91.70% | 0.20% | 1.01% | 7.14% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 98.50% | 0.40% | 0.37% | 0.74% | NA |
| Indica I | 595 | 95.00% | 0.00% | 0.00% | 5.04% | NA |
| Indica II | 465 | 94.40% | 0.60% | 2.15% | 2.80% | NA |
| Indica III | 913 | 91.30% | 0.00% | 0.11% | 8.54% | NA |
| Indica Intermediate | 786 | 87.90% | 0.30% | 2.16% | 9.67% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526665 | A -> G | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.9; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |
| vg0114526665 | A -> DEL | N | N | silent_mutation | Average:44.9; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |