| Variant ID: vg0825998185 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25998185 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
CACCGGCGAGCGCGCGGCGAGCACGGCCCGGTGCGCGTGGAACGTCTCACCGCCGACGGAGAAGGACACGTCCGAGCCGTCGGCGCTGCCCACCATGGCG[C/G]
CGAGCTGGCCGCCCAGGTTAGAGGGCGGCACGGCTATGGCACCACCGTCGCCGAGAATTACGAGCCCACATATGAATGTAGCCATGCCGTCGATCACATA
TATGTGATCGACGGCATGGCTACATTCATATGTGGGCTCGTAATTCTCGGCGACGGTGGTGCCATAGCCGTGCCGCCCTCTAACCTGGGCGGCCAGCTCG[G/C]
CGCCATGGTGGGCAGCGCCGACGGCTCGGACGTGTCCTTCTCCGTCGGCGGTGAGACGTTCCACGCGCACCGGGCCGTGCTCGCCGCGCGCTCGCCGGTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.30% | 0.00% | 16.34% | 13.39% | NA |
| All Indica | 2759 | 52.80% | 0.00% | 25.92% | 21.24% | NA |
| All Japonica | 1512 | 98.80% | 0.00% | 0.40% | 0.79% | NA |
| Aus | 269 | 78.80% | 0.00% | 11.90% | 9.29% | NA |
| Indica I | 595 | 33.60% | 0.00% | 51.26% | 15.13% | NA |
| Indica II | 465 | 56.80% | 0.00% | 21.29% | 21.94% | NA |
| Indica III | 913 | 60.20% | 0.00% | 12.81% | 26.94% | NA |
| Indica Intermediate | 786 | 56.50% | 0.00% | 24.68% | 18.83% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.39% | 1.04% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 1.24% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 12.50% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 0.00% | 7.78% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825998185 | C -> G | LOC_Os08g41150.1 | missense_variant ; p.Gly172Ala; MODERATE | N | Average:72.268; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
| vg0825998185 | C -> G | LOC_Os08g41140.1 | downstream_gene_variant ; 2421.0bp to feature; MODIFIER | N | Average:72.268; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
| vg0825998185 | C -> G | LOC_Os08g41160.1 | downstream_gene_variant ; 951.0bp to feature; MODIFIER | N | Average:72.268; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |