| Variant ID: vg1107679366 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7679366 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGACAATTAATTATATCATGATTGTTGATATGCTAATAGTGACTCGGATTTGTTCTCTGTACTGGTAGGCTTGTGTGATAAAATCTCTGTGGCCAGAATG[C/T]
GGATACTGATGCGGTGATTTTAGAAGGAAAAGAACTGAGTTATATGTGAACAGATGAAAGGCTTACCTGAATTGTCGGAGCTGGAAGGAATGTCAGTCAT
ATGACTGACATTCCTTCCAGCTCCGACAATTCAGGTAAGCCTTTCATCTGTTCACATATAACTCAGTTCTTTTCCTTCTAAAATCACCGCATCAGTATCC[G/A]
CATTCTGGCCACAGAGATTTTATCACACAAGCCTACCAGTACAGAGAACAAATCCGAGTCACTATTAGCATATCAACAATCATGATATAATTAATTGTCT
| 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 | 41.80% | 0.10% | 6.62% | 51.48% | NA |
| All Indica | 2759 | 6.70% | 0.00% | 9.42% | 83.80% | NA |
| All Japonica | 1512 | 92.50% | 0.30% | 2.98% | 4.17% | NA |
| Aus | 269 | 91.10% | 0.00% | 0.74% | 8.18% | NA |
| Indica I | 595 | 6.10% | 0.00% | 7.90% | 86.05% | NA |
| Indica II | 465 | 2.80% | 0.20% | 8.60% | 88.39% | NA |
| Indica III | 913 | 3.60% | 0.00% | 11.17% | 85.21% | NA |
| Indica Intermediate | 786 | 13.20% | 0.00% | 9.03% | 77.74% | NA |
| Temperate Japonica | 767 | 95.80% | 0.70% | 1.17% | 2.35% | NA |
| Tropical Japonica | 504 | 92.10% | 0.00% | 4.96% | 2.98% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 4.56% | 12.45% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 6.67% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107679366 | C -> T | LOC_Os11g13910.1 | upstream_gene_variant ; 1040.0bp to feature; MODIFIER | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1107679366 | C -> T | LOC_Os11g13920.1 | downstream_gene_variant ; 4014.0bp to feature; MODIFIER | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1107679366 | C -> T | LOC_Os11g13900.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1107679366 | C -> DEL | N | N | silent_mutation | Average:4.932; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |