| Variant ID: vg0710348320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10348320 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTGTAATTAGACTTAGTATATAATTATTTACTAGCTAGGGTTGTATAATATACGTCACCTAGACTTAGCTTATATCACGATTTGTAATTAGACTTAGCA[C/T]
GTAAGGTTGTGTAGGGTTCTAATGTACGACATTTACACTTAGCATACATGACTTAGATTGTTAAAACATAAATGTCTCGTGACTTAGCAGATGTTTCTTG
CAAGAAACATCTGCTAAGTCACGAGACATTTATGTTTTAACAATCTAAGTCATGTATGCTAAGTGTAAATGTCGTACATTAGAACCCTACACAACCTTAC[G/A]
TGCTAAGTCTAATTACAAATCGTGATATAAGCTAAGTCTAGGTGACGTATATTATACAACCCTAGCTAGTAAATAATTATATACTAAGTCTAATTACAAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.40% | 2.60% | 3.72% | 63.18% | NA |
| All Indica | 2759 | 5.00% | 0.00% | 4.02% | 91.01% | NA |
| All Japonica | 1512 | 74.30% | 8.30% | 3.97% | 13.49% | NA |
| Aus | 269 | 51.30% | 0.00% | 0.37% | 48.33% | NA |
| Indica I | 595 | 8.20% | 0.00% | 1.34% | 90.42% | NA |
| Indica II | 465 | 5.80% | 0.00% | 1.94% | 92.26% | NA |
| Indica III | 913 | 1.10% | 0.00% | 2.74% | 96.17% | NA |
| Indica Intermediate | 786 | 6.50% | 0.00% | 8.78% | 84.73% | NA |
| Temperate Japonica | 767 | 61.70% | 12.40% | 7.17% | 18.77% | NA |
| Tropical Japonica | 504 | 89.50% | 0.20% | 0.00% | 10.32% | NA |
| Japonica Intermediate | 241 | 82.60% | 12.00% | 2.07% | 3.32% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 2.08% | 94.79% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 2.22% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710348320 | C -> DEL | N | N | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |
| vg0710348320 | C -> T | LOC_Os07g17500.1 | downstream_gene_variant ; 2890.0bp to feature; MODIFIER | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |
| vg0710348320 | C -> T | LOC_Os07g17520.1 | downstream_gene_variant ; 4738.0bp to feature; MODIFIER | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |
| vg0710348320 | C -> T | LOC_Os07g17510.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.963; most accessible tissue: Callus, score: 9.925 | N | N | N | N |