| Variant ID: vg1126364380 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26364380 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 111. )
GGGAGGATGAGGAGAAAACTGCGTTCATTACCCCCGTAGGAACCTATTGTTATACATCAATGCCCTTCGGGTTAAAGAATGCAGGTCCTACTTTTCAACG[A/T]
ACTACTCGAATTTCTTTGGGTAGTCAAATAGGACGTAATGTTGAGGCTTATGTCGATGACTTGGTTGTAAAAACGCGCAACCAAGAAACTTTACTTTCAG
CTGAAAGTAAAGTTTCTTGGTTGCGCGTTTTTACAACCAAGTCATCGACATAAGCCTCAACATTACGTCCTATTTGACTACCCAAAGAAATTCGAGTAGT[T/A]
CGTTGAAAAGTAGGACCTGCATTCTTTAACCCGAAGGGCATTGATGTATAACAATAGGTTCCTACGGGGGTAATGAACGCAGTTTTCTCCTCATCCTCCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 7.90% | 0.50% | 14.09% | 77.53% | NA |
| All Indica | 2759 | 1.30% | 0.50% | 8.41% | 89.74% | NA |
| All Japonica | 1512 | 21.20% | 0.00% | 17.72% | 61.04% | NA |
| Aus | 269 | 0.00% | 2.60% | 50.93% | 46.47% | NA |
| Indica I | 595 | 1.00% | 0.00% | 1.01% | 97.98% | NA |
| Indica II | 465 | 2.60% | 0.90% | 2.15% | 94.41% | NA |
| Indica III | 913 | 0.40% | 0.70% | 13.36% | 85.54% | NA |
| Indica Intermediate | 786 | 1.80% | 0.60% | 11.96% | 85.62% | NA |
| Temperate Japonica | 767 | 33.00% | 0.00% | 14.99% | 52.02% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 15.87% | 80.75% | NA |
| Japonica Intermediate | 241 | 21.20% | 0.00% | 30.29% | 48.55% | NA |
| VI/Aromatic | 96 | 3.10% | 2.10% | 16.67% | 78.12% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 14.44% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126364380 | A -> T | LOC_Os11g43670.1 | synonymous_variant ; p.Arg963Arg; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1126364380 | A -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |