| Variant ID: vg1117780472 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17780472 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 336. )
ACTGGGTGCTTTTACTCTTCGACCTGGAGGCCTGCACCGTCAACGTATATGACTCAATGGATAAAAAAGAGTCTACGTTTGACAAGGTTTTCGAACTTAT[A/C]
GACAGGTACCGTCATAAGTTCCTTTGTTAATTAAGAAAATCTTGTTATGTTAATTGCTACTACGAATCATAGCTTTAAACTCTATGTAGGGCTTGGTATC
GATACCAAGCCCTACATAGAGTTTAAAGCTATGATTCGTAGTAGCAATTAACATAACAAGATTTTCTTAATTAACAAAGGAACTTATGACGGTACCTGTC[T/G]
ATAAGTTCGAAAACCTTGTCAAACGTAGACTCTTTTTTATCCATTGAGTCATATACGTTGACGGTGCAGGCCTCCAGGTCGAAGAGTAAAAGCACCCAGT
| 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 | 25.10% | 0.10% | 0.99% | 73.80% | NA |
| All Indica | 2759 | 8.40% | 0.00% | 0.47% | 91.12% | NA |
| All Japonica | 1512 | 53.50% | 0.30% | 1.46% | 44.71% | NA |
| Aus | 269 | 10.00% | 0.00% | 3.72% | 86.25% | NA |
| Indica I | 595 | 6.20% | 0.00% | 0.00% | 93.78% | NA |
| Indica II | 465 | 23.20% | 0.00% | 1.29% | 75.48% | NA |
| Indica III | 913 | 2.60% | 0.00% | 0.11% | 97.26% | NA |
| Indica Intermediate | 786 | 8.00% | 0.00% | 0.76% | 91.22% | NA |
| Temperate Japonica | 767 | 61.70% | 0.40% | 2.74% | 35.20% | NA |
| Tropical Japonica | 504 | 28.00% | 0.00% | 0.20% | 71.83% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.80% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 2.22% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117780472 | A -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1117780472 | A -> C | LOC_Os11g30552.1 | synonymous_variant ; p.Ile1047Ile; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |