| Variant ID: vg0710348222 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10348222 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 126. )
TCGTGACTTAGCATATACACACGAAACACTTAGCATATACATGACTATTTTAGTCTTAGCATGTAATATTATTTGAGTTTTAATATAAGATTATTTTATT[T/G]
GTAATTAGACTTAGTATATAATTATTTACTAGCTAGGGTTGTATAATATACGTCACCTAGACTTAGCTTATATCACGATTTGTAATTAGACTTAGCACGT
ACGTGCTAAGTCTAATTACAAATCGTGATATAAGCTAAGTCTAGGTGACGTATATTATACAACCCTAGCTAGTAAATAATTATATACTAAGTCTAATTAC[A/C]
AATAAAATAATCTTATATTAAAACTCAAATAATATTACATGCTAAGACTAAAATAGTCATGTATATGCTAAGTGTTTCGTGTGTATATGCTAAGTCACGA
| 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 | 19.90% | 12.00% | 4.19% | 63.94% | NA |
| All Indica | 2759 | 2.80% | 0.60% | 4.20% | 92.39% | NA |
| All Japonica | 1512 | 53.70% | 28.30% | 4.63% | 13.36% | NA |
| Aus | 269 | 8.90% | 40.10% | 2.97% | 47.96% | NA |
| Indica I | 595 | 5.20% | 0.30% | 3.36% | 91.09% | NA |
| Indica II | 465 | 4.50% | 0.40% | 1.72% | 93.33% | NA |
| Indica III | 913 | 0.40% | 0.00% | 1.86% | 97.70% | NA |
| Indica Intermediate | 786 | 2.80% | 1.50% | 9.03% | 86.64% | NA |
| Temperate Japonica | 767 | 75.70% | 0.70% | 5.08% | 18.51% | NA |
| Tropical Japonica | 504 | 19.80% | 67.70% | 2.18% | 10.32% | NA |
| Japonica Intermediate | 241 | 54.40% | 34.00% | 8.30% | 3.32% | NA |
| VI/Aromatic | 96 | 2.10% | 1.00% | 3.12% | 93.75% | NA |
| Intermediate | 90 | 25.60% | 15.60% | 1.11% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710348222 | T -> DEL | N | N | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |
| vg0710348222 | T -> G | LOC_Os07g17500.1 | downstream_gene_variant ; 2792.0bp to feature; MODIFIER | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |
| vg0710348222 | T -> G | LOC_Os07g17520.1 | downstream_gene_variant ; 4836.0bp to feature; MODIFIER | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |
| vg0710348222 | T -> G | LOC_Os07g17510.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |