| Variant ID: vg1107555931 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7555931 |
| 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: 304. )
CCATGTACAGCTGATGGAACTTGTACATTTGTGTGGGTAGGGACTGCAGCAGCTCAGGCTTGACAAGCGGTTTACCGAGTTCGTACATGTATTTCACTTC[C/T]
GCCTTTTCGATTGGTGCGACTCCTAGCAATTGATCCGTAGTTAGACCGGTGTCAGTAATAAATTGTTCTATCGTCATTTCTTTACCGGTCACCAACGGCT
AGCCGTTGGTGACCGGTAAAGAAATGACGATAGAACAATTTATTACTGACACCGGTCTAACTACGGATCAATTGCTAGGAGTCGCACCAATCGAAAAGGC[G/A]
GAAGTGAAATACATGTACGAACTCGGTAAACCGCTTGTCAAGCCTGAGCTGCTGCAGTCCCTACCCACACAAATGTACAAGTTCCATCAGCTGTACATGG
| 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 | 1.70% | 1.00% | 6.79% | 90.54% | NA |
| All Indica | 2759 | 0.10% | 0.20% | 0.40% | 99.31% | NA |
| All Japonica | 1512 | 4.70% | 2.80% | 19.84% | 72.69% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.65% | 99.14% | NA |
| Indica III | 913 | 0.10% | 0.10% | 0.00% | 99.78% | NA |
| Indica Intermediate | 786 | 0.10% | 0.50% | 1.02% | 98.35% | NA |
| Temperate Japonica | 767 | 3.30% | 1.30% | 24.12% | 71.32% | NA |
| Tropical Japonica | 504 | 6.90% | 1.60% | 13.10% | 78.37% | NA |
| Japonica Intermediate | 241 | 4.60% | 10.00% | 20.33% | 65.15% | NA |
| VI/Aromatic | 96 | 2.10% | 1.00% | 5.21% | 91.67% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 5.56% | 92.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107555931 | C -> T | LOC_Os11g13730.1 | synonymous_variant ; p.Ala832Ala; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1107555931 | C -> DEL | LOC_Os11g13730.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |