| Variant ID: vg1101693903 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1693903 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, G: 0.01, others allele: 0.00, population size: 241. )
ATGTAAGGAAGAAATGCTCTTTAAATTGTGTTCATGCAAAACAGATGAAATCGATAAAGCTGAAAATATTTGTCCTATCAAGAGACGCTGAATGCATTTT[T/G]
CACATGTAGGATGGGCGGATAGATTATTCAGAGTTTGTGGCCATGATGAGGAAAGGATCAGGCTGTGCAGAAGCAACAAACCCAAAGAAGAAGAGGCGAG
CTCGCCTCTTCTTCTTTGGGTTTGTTGCTTCTGCACAGCCTGATCCTTTCCTCATCATGGCCACAAACTCTGAATAATCTATCCGCCCATCCTACATGTG[A/C]
AAAATGCATTCAGCGTCTCTTGATAGGACAAATATTTTCAGCTTTATCGATTTCATCTGTTTTGCATGAACACAATTTAAAGAGCATTTCTTCCTTACAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.00% | 0.10% | 5.52% | 27.40% | NA |
| All Indica | 2759 | 47.20% | 0.00% | 8.26% | 44.51% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 68.80% | 0.00% | 10.04% | 21.19% | NA |
| Indica I | 595 | 61.30% | 0.20% | 9.08% | 29.41% | NA |
| Indica II | 465 | 54.00% | 0.00% | 6.67% | 39.35% | NA |
| Indica III | 913 | 29.80% | 0.00% | 9.31% | 60.90% | NA |
| Indica Intermediate | 786 | 52.70% | 0.00% | 7.38% | 39.95% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | 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 | 86.70% | 3.30% | 6.67% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101693903 | T -> DEL | N | N | silent_mutation | Average:28.15; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| vg1101693903 | T -> G | LOC_Os11g04160.1 | downstream_gene_variant ; 2563.0bp to feature; MODIFIER | silent_mutation | Average:28.15; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| vg1101693903 | T -> G | LOC_Os11g04174.1 | downstream_gene_variant ; 569.0bp to feature; MODIFIER | silent_mutation | Average:28.15; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| vg1101693903 | T -> G | LOC_Os11g04180.1 | downstream_gene_variant ; 2524.0bp to feature; MODIFIER | silent_mutation | Average:28.15; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| vg1101693903 | T -> G | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:28.15; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |