| Variant ID: vg0114526624 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526624 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, A: 0.34, others allele: 0.00, population size: 186. )
CACGTTGATTTTCTGTTTAGGGGAAATTTTAGAGTTGTGTTTTTCTGCTAGGGAATAGATGGTTCTCCAAGTTAGCTCTTATTTGTCGGACTGCAGGAAT[A/C]
GTTCTGCAAATAAGAAACACATGATCAAAACTAGAAAAGAAGCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTGAAGATTCACCAAA
TTTGGTGAATCTTCAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGCTTCTTTTCTAGTTTTGATCATGTGTTTCTTATTTGCAGAAC[T/G]
ATTCCTGCAGTCCGACAAATAAGAGCTAACTTGGAGAACCATCTATTCCCTAGCAGAAAAACACAACTCTAAAATTTCCCCTAAACAGAAAATCAACGTG
| 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 | 79.60% | 15.40% | 0.11% | 4.89% | NA |
| All Indica | 2759 | 68.10% | 23.60% | 0.14% | 8.19% | NA |
| All Japonica | 1512 | 97.50% | 2.40% | 0.00% | 0.07% | NA |
| Aus | 269 | 86.60% | 11.90% | 0.37% | 1.12% | NA |
| Indica I | 595 | 80.30% | 14.60% | 0.00% | 5.04% | NA |
| Indica II | 465 | 81.10% | 13.50% | 0.22% | 5.16% | NA |
| Indica III | 913 | 54.90% | 36.40% | 0.22% | 8.54% | NA |
| Indica Intermediate | 786 | 66.50% | 21.40% | 0.13% | 11.96% | NA |
| Temperate Japonica | 767 | 98.70% | 1.20% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526624 | A -> DEL | LOC_Os01g25630.1 | N | frameshift_variant | Average:43.334; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |
| vg0114526624 | A -> C | LOC_Os01g25630.1 | missense_variant ; p.Leu1024Arg; MODERATE | nonsynonymous_codon ; L1024R | Average:43.334; most accessible tissue: Zhenshan97 flower, score: 75.194 | unknown | unknown | TOLERATED | 0.25 |