| Variant ID: vg1104670157 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 4670157 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )
ACCGGTTTCAATATTTTCCCAGCGAGATCATTCATAGCCTGCAAAACATGGTGGAAGTGAACCGACACTGTCGAGTTGGAGCGGACCCACCGATTGTTCG[C/T]
GTCTCTGATTGGACGATTTCCACCCATCGTGTACAAGAAAATACCAAGCTTTTCCATGGAACAGACCCCTGCTGTTCCTACAAGACCAAAAGAAGTGACC
GGTCACTTCTTTTGGTCTTGTAGGAACAGCAGGGGTCTGTTCCATGGAAAAGCTTGGTATTTTCTTGTACACGATGGGTGGAAATCGTCCAATCAGAGAC[G/A]
CGAACAATCGGTGGGTCCGCTCCAACTCGACAGTGTCGGTTCACTTCCACCATGTTTTGCAGGCTATGAATGATCTCGCTGGGAAAATATTGAAACCGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.10% | 2.60% | 25.07% | 66.29% | NA |
| All Indica | 2759 | 3.30% | 0.10% | 11.96% | 84.67% | NA |
| All Japonica | 1512 | 12.80% | 6.70% | 49.74% | 30.75% | NA |
| Aus | 269 | 0.00% | 0.00% | 2.60% | 97.40% | NA |
| Indica I | 595 | 4.50% | 0.00% | 11.43% | 84.03% | NA |
| Indica II | 465 | 1.70% | 0.00% | 5.59% | 92.69% | NA |
| Indica III | 913 | 2.80% | 0.00% | 14.68% | 82.48% | NA |
| Indica Intermediate | 786 | 3.80% | 0.30% | 12.98% | 82.95% | NA |
| Temperate Japonica | 767 | 15.30% | 9.50% | 47.07% | 28.16% | NA |
| Tropical Japonica | 504 | 3.80% | 4.00% | 55.95% | 36.31% | NA |
| Japonica Intermediate | 241 | 23.70% | 3.70% | 45.23% | 27.39% | NA |
| VI/Aromatic | 96 | 0.00% | 13.50% | 60.42% | 26.04% | NA |
| Intermediate | 90 | 3.30% | 4.40% | 42.22% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1104670157 | C -> T | LOC_Os11g08790.1 | missense_variant ; p.Ala113Thr; MODERATE | nonsynonymous_codon ; A113T | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.51 |
| vg1104670157 | C -> DEL | LOC_Os11g08790.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |