| Variant ID: vg1115079712 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079712 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGCTCAGATGAGTTATGTTTGTTTCTGAATTTCTGTCTTTGTTTCTGAATTTCTGTCTCCCACAAGGTTACCTTGGTTATACTGCACAATATCCAAATTT[G/T,A]
CTATACACGGTCTCTCATATTTATTAATTTCTTCAGTTTGTCCAATTTCCCATATGAATTTTGAAAAATAAGAAACACCTTCCATGGGAATACCAATATA
TATATTGGTATTCCCATGGAAGGTGTTTCTTATTTTTCAAAATTCATATGGGAAATTGGACAAACTGAAGAAATTAATAAATATGAGAGACCGTGTATAG[C/A,T]
AAATTTGGATATTGTGCAGTATAACCAAGGTAACCTTGTGGGAGACAGAAATTCAGAAACAAAGACAGAAATTCAGAAACAAACATAACTCATCTGAGCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 0.30% | 0.85% | 0.00% | NA |
| All Indica | 2759 | 98.00% | 0.50% | 1.45% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.80% | 1.00% | 6.22% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.60% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.60% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079712 | G -> T | LOC_Os11g26340.1 | downstream_gene_variant ; 3746.0bp to feature; MODIFIER | silent_mutation | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1115079712 | G -> T | LOC_Os11g26360.1 | downstream_gene_variant ; 3118.0bp to feature; MODIFIER | silent_mutation | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1115079712 | G -> T | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1115079712 | G -> A | LOC_Os11g26340.1 | downstream_gene_variant ; 3746.0bp to feature; MODIFIER | N | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1115079712 | G -> A | LOC_Os11g26360.1 | downstream_gene_variant ; 3118.0bp to feature; MODIFIER | N | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1115079712 | G -> A | LOC_Os11g26350.1 | intron_variant ; MODIFIER | N | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |