| Variant ID: vg1104669356 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 4669356 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 218. )
AGCGGCCTCGCTATTTGTTGCGTAATACATATGGTCGAATGAATCGTTCAGCAGCGGCACTGGATTGCCGTTGTAGAGAGCATTAGTGAACCGATAGGTC[G/A]
GATCTTTACTATCCAACCTAAAGTTGTGTAGAGCGAAAGCTGCATGAATGATGCGTGCAGGGATGTCCTCATCTCGGTAATAAGGGATTTCTTTCAATAT
ATATTGAAAGAAATCCCTTATTACCGAGATGAGGACATCCCTGCACGCATCATTCATGCAGCTTTCGCTCTACACAACTTTAGGTTGGATAGTAAAGATC[C/T]
GACCTATCGGTTCACTAATGCTCTCTACAACGGCAATCCAGTGCCGCTGCTGAACGATTCATTCGACCATATGTATTACGCAACAAATAGCGAGGCCGCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.90% | 0.40% | 6.43% | 52.22% | NA |
| All Indica | 2759 | 20.90% | 0.70% | 7.83% | 70.64% | NA |
| All Japonica | 1512 | 80.70% | 0.10% | 2.78% | 16.47% | NA |
| Aus | 269 | 4.50% | 0.00% | 9.67% | 85.87% | NA |
| Indica I | 595 | 25.00% | 0.00% | 3.36% | 71.60% | NA |
| Indica II | 465 | 10.50% | 0.00% | 11.83% | 77.63% | NA |
| Indica III | 913 | 22.70% | 1.50% | 8.11% | 67.69% | NA |
| Indica Intermediate | 786 | 21.80% | 0.50% | 8.52% | 69.21% | NA |
| Temperate Japonica | 767 | 79.10% | 0.00% | 1.96% | 18.90% | NA |
| Tropical Japonica | 504 | 82.30% | 0.00% | 4.37% | 13.29% | NA |
| Japonica Intermediate | 241 | 82.20% | 0.40% | 2.07% | 15.35% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 11.46% | 8.33% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 10.00% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1104669356 | G -> A | LOC_Os11g08790.1 | missense_variant ; p.Pro346Leu; MODERATE | nonsynonymous_codon ; P346L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.33 |
| vg1104669356 | G -> DEL | LOC_Os11g08790.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |