| Variant ID: vg1115079449 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079449 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTACTGCTATTGATTTCCCAGGCATAAATTCATATTATTTTTGTATACATATATAGACGTATCCCGTATCCATGTTTTTCAGAAAATGATGTATCCTATC[C/G]
ATATCCGTATCCCTGTATCTCGGTAACATAGAGCAAAGGATGTTGCTTGCTGCAGATGGGGTGACGGCCGCAGCGGCAGCGACAGTGAGTAGTTTAGAAC
GTTCTAAACTACTCACTGTCGCTGCCGCTGCGGCCGTCACCCCATCTGCAGCAAGCAACATCCTTTGCTCTATGTTACCGAGATACAGGGATACGGATAT[G/C]
GATAGGATACATCATTTTCTGAAAAACATGGATACGGGATACGTCTATATATGTATACAAAAATAATATGAATTTATGCCTGGGAAATCAATAGCAGTAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.70% | 0.00% | 8.53% | 2.73% | NA |
| All Indica | 2759 | 81.80% | 0.00% | 14.06% | 4.13% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.46% | 0.46% | NA |
| Aus | 269 | 95.90% | 0.40% | 1.49% | 2.23% | NA |
| Indica I | 595 | 76.10% | 0.00% | 17.14% | 6.72% | NA |
| Indica II | 465 | 88.60% | 0.00% | 10.97% | 0.43% | NA |
| Indica III | 913 | 82.10% | 0.10% | 13.69% | 4.05% | NA |
| Indica Intermediate | 786 | 81.60% | 0.00% | 13.99% | 4.45% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.65% | 0.39% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079449 | C -> DEL | N | N | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079449 | C -> G | LOC_Os11g26340.1 | downstream_gene_variant ; 3483.0bp to feature; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079449 | C -> G | LOC_Os11g26360.1 | downstream_gene_variant ; 3381.0bp to feature; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079449 | C -> G | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |