| Variant ID: vg0509254204 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9254204 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 232. )
GTCTTAATTAGACTTAGCATATACGCACGAAACACTTAGCATATACATGACTATTGTAGTCTTAGCATGTAATATTATTTGAGTTTTAATATAAGATTAT[T/G]
TTATTTGTAATTAGACTTAGTATATAATTATTTACTAGCTAGGGTTGTATAATATACGTCACCTAGACTTAGCTTATATCACGATTTGTAATTAGACTTA
TAAGTCTAATTACAAATCGTGATATAAGCTAAGTCTAGGTGACGTATATTATACAACCCTAGCTAGTAAATAATTATATACTAAGTCTAATTACAAATAA[A/C]
ATAATCTTATATTAAAACTCAAATAATATTACATGCTAAGACTACAATAGTCATGTATATGCTAAGTGTTTCGTGCGTATATGCTAAGTCTAATTAAGAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.30% | 0.10% | 4.00% | 1.61% | NA |
| All Indica | 2759 | 93.10% | 0.10% | 5.65% | 1.12% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 73.20% | 0.00% | 10.41% | 16.36% | NA |
| Indica I | 595 | 95.50% | 0.00% | 4.54% | 0.00% | NA |
| Indica II | 465 | 84.30% | 0.20% | 15.27% | 0.22% | NA |
| Indica III | 913 | 94.00% | 0.20% | 4.38% | 1.42% | NA |
| Indica Intermediate | 786 | 95.40% | 0.10% | 2.29% | 2.16% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | 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% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509254204 | T -> DEL | N | N | silent_mutation | Average:14.694; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0509254204 | T -> G | LOC_Os05g16330.1 | downstream_gene_variant ; 2544.0bp to feature; MODIFIER | silent_mutation | Average:14.694; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0509254204 | T -> G | LOC_Os05g16340.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.694; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |