| Variant ID: vg0135357580 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35357580 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATACAACACCGAATAGTTCGCAATACTACTAGTACAACAATAGTCGGAGGTACTCATTACAACAACATTCAATTGAAATTACACGATACAAGTATTTAGT[C/G]
CGAACACTCATCACATCACAACAACATTTTATTTCCTAAATCGATAGCATTGTTACACCATGGAATCGCCTGCTGCGCGACGACGCCTTGGCCTTGCGCG
CGCGCAAGGCCAAGGCGTCGTCGCGCAGCAGGCGATTCCATGGTGTAACAATGCTATCGATTTAGGAAATAAAATGTTGTTGTGATGTGATGAGTGTTCG[G/C]
ACTAAATACTTGTATCGTGTAATTTCAATTGAATGTTGTTGTAATGAGTACCTCCGACTATTGTTGTACTAGTAGTATTGCGAACTATTCGGTGTTGTAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.60% | 0.10% | 18.75% | 26.60% | NA |
| All Indica | 2759 | 45.10% | 0.10% | 27.04% | 27.69% | NA |
| All Japonica | 1512 | 65.80% | 0.00% | 4.96% | 29.23% | NA |
| Aus | 269 | 69.90% | 0.00% | 17.10% | 13.01% | NA |
| Indica I | 595 | 36.80% | 0.00% | 43.03% | 20.17% | NA |
| Indica II | 465 | 37.40% | 0.90% | 27.10% | 34.62% | NA |
| Indica III | 913 | 54.80% | 0.00% | 15.44% | 29.79% | NA |
| Indica Intermediate | 786 | 44.80% | 0.00% | 28.37% | 26.84% | NA |
| Temperate Japonica | 767 | 57.20% | 0.00% | 1.83% | 40.94% | NA |
| Tropical Japonica | 504 | 70.60% | 0.00% | 11.31% | 18.06% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 1.66% | 15.35% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 3.12% | 2.08% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 17.78% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135357580 | C -> G | LOC_Os01g61100.1 | upstream_gene_variant ; 4851.0bp to feature; MODIFIER | silent_mutation | Average:10.56; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0135357580 | C -> G | LOC_Os01g61090.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.56; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0135357580 | C -> DEL | N | N | silent_mutation | Average:10.56; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |