| Variant ID: vg0509254267 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9254267 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 227. )
AGCATGTAATATTATTTGAGTTTTAATATAAGATTATTTTATTTGTAATTAGACTTAGTATATAATTATTTACTAGCTAGGGTTGTATAATATACGTCAC[C/A]
TAGACTTAGCTTATATCACGATTTGTAATTAGACTTAGCACGTAAGGTTGTGTAGGGTTCTAATGTACGACATTTACACTTAGCATACATGACTTAGATT
AATCTAAGTCATGTATGCTAAGTGTAAATGTCGTACATTAGAACCCTACACAACCTTACGTGCTAAGTCTAATTACAAATCGTGATATAAGCTAAGTCTA[G/T]
GTGACGTATATTATACAACCCTAGCTAGTAAATAATTATATACTAAGTCTAATTACAAATAAAATAATCTTATATTAAAACTCAAATAATATTACATGCT
| 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 | 91.00% | 0.00% | 3.28% | 5.71% | NA |
| All Indica | 2759 | 88.30% | 0.00% | 4.60% | 7.10% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 64.30% | 0.00% | 10.41% | 25.28% | NA |
| Indica I | 595 | 93.60% | 0.00% | 1.68% | 4.71% | NA |
| Indica II | 465 | 76.80% | 0.00% | 7.10% | 16.13% | NA |
| Indica III | 913 | 87.50% | 0.00% | 6.24% | 6.24% | NA |
| Indica Intermediate | 786 | 92.00% | 0.00% | 3.44% | 4.58% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509254267 | C -> A | LOC_Os05g16330.1 | downstream_gene_variant ; 2607.0bp to feature; MODIFIER | N | Average:16.798; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
| vg0509254267 | C -> A | LOC_Os05g16340.1 | intron_variant ; MODIFIER | N | Average:16.798; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |