| Variant ID: vg0509254201 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9254201 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 236. )
GTAGTCTTAATTAGACTTAGCATATACGCACGAAACACTTAGCATATACATGACTATTGTAGTCTTAGCATGTAATATTATTTGAGTTTTAATATAAGAT[T/A]
ATTTTATTTGTAATTAGACTTAGTATATAATTATTTACTAGCTAGGGTTGTATAATATACGTCACCTAGACTTAGCTTATATCACGATTTGTAATTAGAC
GTCTAATTACAAATCGTGATATAAGCTAAGTCTAGGTGACGTATATTATACAACCCTAGCTAGTAAATAATTATATACTAAGTCTAATTACAAATAAAAT[A/T]
ATCTTATATTAAAACTCAAATAATATTACATGCTAAGACTACAATAGTCATGTATATGCTAAGTGTTTCGTGCGTATATGCTAAGTCTAATTAAGACTAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.30% | 0.10% | 3.87% | 1.76% | NA |
| All Indica | 2759 | 93.00% | 0.10% | 5.47% | 1.38% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 73.60% | 0.00% | 10.04% | 16.36% | NA |
| Indica I | 595 | 95.50% | 0.00% | 4.20% | 0.34% | NA |
| Indica II | 465 | 84.10% | 0.20% | 14.41% | 1.29% | NA |
| Indica III | 913 | 94.00% | 0.20% | 4.49% | 1.31% | NA |
| Indica Intermediate | 786 | 95.30% | 0.10% | 2.29% | 2.29% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0509254201 | T -> DEL | N | N | silent_mutation | Average:14.122; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | N | N | N | N |
| vg0509254201 | T -> A | LOC_Os05g16330.1 | downstream_gene_variant ; 2541.0bp to feature; MODIFIER | silent_mutation | Average:14.122; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | N | N | N | N |
| vg0509254201 | T -> A | LOC_Os05g16340.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.122; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | N | N | N | N |