| Variant ID: vg1112795069 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12795069 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAGGAATTTAATACAAATGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTT[T/C]
AATCTATCAAAACCCAAGAAACCCTGAAGGGGTACCTAACTATTTATAGAGGTGGGAGGACGACCAAGAGGGTCCAAGGGTCGTGCTCCACCAGATTGGG
CCCAATCTGGTGGAGCACGACCCTTGGACCCTCTTGGTCGTCCTCCCACCTCTATAAATAGTTAGGTACCCCTTCAGGGTTTCTTGGGTTTTGATAGATT[A/G]
AAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCATTTGTATTAAATTCCTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.20% | 0.20% | 28.95% | 35.67% | NA |
| All Indica | 2759 | 3.60% | 0.20% | 44.04% | 52.16% | NA |
| All Japonica | 1512 | 94.90% | 0.00% | 1.06% | 4.03% | NA |
| Aus | 269 | 3.30% | 0.70% | 42.75% | 53.16% | NA |
| Indica I | 595 | 4.70% | 0.20% | 33.61% | 61.51% | NA |
| Indica II | 465 | 3.40% | 0.40% | 16.56% | 79.57% | NA |
| Indica III | 913 | 1.90% | 0.00% | 68.78% | 29.35% | NA |
| Indica Intermediate | 786 | 5.00% | 0.30% | 39.44% | 55.34% | NA |
| Temperate Japonica | 767 | 96.20% | 0.00% | 1.17% | 2.61% | NA |
| Tropical Japonica | 504 | 91.70% | 0.00% | 0.99% | 7.34% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 6.25% | 7.29% | NA |
| Intermediate | 90 | 41.10% | 1.10% | 17.78% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1112795069 | T -> DEL | N | N | silent_mutation | Average:9.396; most accessible tissue: Zhenshan97 flag leaf, score: 15.278 | N | N | N | N |
| vg1112795069 | T -> C | LOC_Os11g22310.1 | upstream_gene_variant ; 1759.0bp to feature; MODIFIER | silent_mutation | Average:9.396; most accessible tissue: Zhenshan97 flag leaf, score: 15.278 | N | N | N | N |
| vg1112795069 | T -> C | LOC_Os11g22330.1 | upstream_gene_variant ; 3604.0bp to feature; MODIFIER | silent_mutation | Average:9.396; most accessible tissue: Zhenshan97 flag leaf, score: 15.278 | N | N | N | N |
| vg1112795069 | T -> C | LOC_Os11g22320.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.396; most accessible tissue: Zhenshan97 flag leaf, score: 15.278 | N | N | N | N |