| Variant ID: vg0420972028 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20972028 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )
GTACTAGTAAGTAATCTATGCAAACTCCAATCCTTACATGTCATACCAATTTCTGCATGATTTGCAGTCAAGCAGTACCGTCTTTTGCATAATACACAGC[G/A]
GATATGCACTCATATGAGTACAGAGGCGTGTTTTTACTCAATAATGGAGAGTTTTGCATCCTAGTGAAGTGTGTACAAAGCAAGGAGCATCTCTCTCATA
TATGAGAGAGATGCTCCTTGCTTTGTACACACTTCACTAGGATGCAAAACTCTCCATTATTGAGTAAAAACACGCCTCTGTACTCATATGAGTGCATATC[C/T]
GCTGTGTATTATGCAAAAGACGGTACTGCTTGACTGCAAATCATGCAGAAATTGGTATGACATGTAAGGATTGGAGTTTGCATAGATTACTTACTAGTAC
| 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 | 38.10% | 16.60% | 3.34% | 41.98% | NA |
| All Indica | 2759 | 9.00% | 27.90% | 3.99% | 59.12% | NA |
| All Japonica | 1512 | 91.30% | 0.10% | 1.19% | 7.34% | NA |
| Aus | 269 | 23.40% | 0.70% | 1.49% | 74.35% | NA |
| Indica I | 595 | 22.70% | 52.80% | 1.85% | 22.69% | NA |
| Indica II | 465 | 6.90% | 7.70% | 3.44% | 81.94% | NA |
| Indica III | 913 | 2.10% | 27.90% | 5.91% | 64.07% | NA |
| Indica Intermediate | 786 | 7.80% | 21.10% | 3.69% | 67.43% | NA |
| Temperate Japonica | 767 | 99.50% | 0.30% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 78.40% | 0.00% | 3.17% | 18.45% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 0.41% | 7.05% | NA |
| VI/Aromatic | 96 | 52.10% | 5.20% | 20.83% | 21.88% | NA |
| Intermediate | 90 | 64.40% | 5.60% | 6.67% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420972028 | G -> DEL | N | N | silent_mutation | Average:11.411; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0420972028 | G -> A | LOC_Os04g34680.1 | downstream_gene_variant ; 4335.0bp to feature; MODIFIER | silent_mutation | Average:11.411; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0420972028 | G -> A | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.411; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |