| Variant ID: vg0825998195 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25998195 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
CGCGCGGCGAGCACGGCCCGGTGCGCGTGGAACGTCTCACCGCCGACGGAGAAGGACACGTCCGAGCCGTCGGCGCTGCCCACCATGGCGCCGAGCTGGC[C/T]
GCCCAGGTTAGAGGGCGGCACGGCTATGGCACCACCGTCGCCGAGAATTACGAGCCCACATATGAATGTAGCCATGCCGTCGATCACATAAATCGACTCG
CGAGTCGATTTATGTGATCGACGGCATGGCTACATTCATATGTGGGCTCGTAATTCTCGGCGACGGTGGTGCCATAGCCGTGCCGCCCTCTAACCTGGGC[G/A]
GCCAGCTCGGCGCCATGGTGGGCAGCGCCGACGGCTCGGACGTGTCCTTCTCCGTCGGCGGTGAGACGTTCCACGCGCACCGGGCCGTGCTCGCCGCGCG
| 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 | 90.50% | 0.00% | 6.86% | 2.62% | NA |
| All Indica | 2759 | 84.70% | 0.00% | 10.98% | 4.28% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.33% | 0.07% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.74% | 0.37% | NA |
| Indica I | 595 | 73.30% | 0.00% | 25.55% | 1.18% | NA |
| Indica II | 465 | 85.20% | 0.00% | 10.11% | 4.73% | NA |
| Indica III | 913 | 91.80% | 0.00% | 2.30% | 5.91% | NA |
| Indica Intermediate | 786 | 85.00% | 0.00% | 10.56% | 4.45% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 10.42% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 4.44% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825998195 | C -> T | LOC_Os08g41150.1 | missense_variant ; p.Gly169Ser; MODERATE | N | Average:71.96; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
| vg0825998195 | C -> T | LOC_Os08g41140.1 | downstream_gene_variant ; 2431.0bp to feature; MODIFIER | N | Average:71.96; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
| vg0825998195 | C -> T | LOC_Os08g41160.1 | downstream_gene_variant ; 941.0bp to feature; MODIFIER | N | Average:71.96; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |