| Variant ID: vg1101693413 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1693413 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 336. )
GGGACCATTACGCTTGAGGAGCTCAAAAATGGGTTAGCAAAGCAGGGCACCAAGTTTTCAGACAACGAAATTGAGCAACTGATGGAAGCAGTGAGTCCTC[A/G]
TAGTGAAGCTACAAACTTAGTTCAGTTCGAGATGAAATGCTAAAACTGACAGGACTCCTGGAAATTCCTTTCAACTTTCAGGCTGATGCTGATGGCAATG
CATTGCCATCAGCATCAGCCTGAAAGTTGAAAGGAATTTCCAGGAGTCCTGTCAGTTTTAGCATTTCATCTCGAACTGAACTAAGTTTGTAGCTTCACTA[T/C]
GAGGACTCACTGCTTCCATCAGTTGCTCAATTTCGTTGTCTGAAAACTTGGTGCCCTGCTTTGCTAACCCATTTTTGAGCTCCTCAAGCGTAATGGTCCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101693413 | A -> G | LOC_Os11g04160.1 | downstream_gene_variant ; 2073.0bp to feature; MODIFIER | silent_mutation | Average:36.999; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1101693413 | A -> G | LOC_Os11g04174.1 | downstream_gene_variant ; 1059.0bp to feature; MODIFIER | silent_mutation | Average:36.999; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1101693413 | A -> G | LOC_Os11g04180.1 | downstream_gene_variant ; 3014.0bp to feature; MODIFIER | silent_mutation | Average:36.999; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1101693413 | A -> G | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.999; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |