| Variant ID: vg1112794952 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12794952 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGCGATCGATACACCTCTCCGTGGGTTGTTGATCTTGCCGGTGCAGATCAACCCTATTCCTGCAAGCAAATCGAAGAAACAAGCAAGAACAAGATAAAAG[A/C]
AATATGATATTGCAAATAGGAATTTAATACAAATGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGT
ACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCATTTGTATTAAATTCCTATTTGCAATATCATATT[T/G]
CTTTTATCTTGTTCTTGCTTGTTTCTTCGATTTGCTTGCAGGAATAGGGTTGATCTGCACCGGCAAGATCAACAACCCACGGAGAGGTGTATCGATCGCT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.80% | 0.40% | 47.91% | 15.87% | NA |
| All Indica | 2759 | 4.90% | 0.50% | 72.56% | 21.96% | NA |
| All Japonica | 1512 | 94.80% | 0.20% | 2.58% | 2.38% | NA |
| Aus | 269 | 1.90% | 0.00% | 65.06% | 33.09% | NA |
| Indica I | 595 | 4.50% | 0.30% | 59.66% | 35.46% | NA |
| Indica II | 465 | 4.70% | 0.60% | 57.85% | 36.77% | NA |
| Indica III | 913 | 4.10% | 0.80% | 91.57% | 3.61% | NA |
| Indica Intermediate | 786 | 6.40% | 0.40% | 68.96% | 24.30% | NA |
| Temperate Japonica | 767 | 96.10% | 0.40% | 2.61% | 0.91% | NA |
| Tropical Japonica | 504 | 91.70% | 0.00% | 2.98% | 5.36% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 11.46% | 3.12% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 41.11% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1112794952 | A -> DEL | N | N | silent_mutation | Average:9.614; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | N | N | N | N |
| vg1112794952 | A -> C | LOC_Os11g22310.1 | upstream_gene_variant ; 1642.0bp to feature; MODIFIER | silent_mutation | Average:9.614; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | N | N | N | N |
| vg1112794952 | A -> C | LOC_Os11g22330.1 | upstream_gene_variant ; 3721.0bp to feature; MODIFIER | silent_mutation | Average:9.614; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | N | N | N | N |
| vg1112794952 | A -> C | LOC_Os11g22320.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.614; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | N | N | N | N |