| Variant ID: vg1126364023 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26364023 |
| 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: 127. )
CCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCG[C/T]
GAGGAGGTGGCGAGACTTCTGGAGGCCGGATTCATCCGTGAAGTCATCCATCCGGAGTGGCTGGCGAACCCGGTGGTCGTTCCCAAGGCGAACGGCAAGC
GCTTGCCGTTCGCCTTGGGAACGACCACCGGGTTCGCCAGCCACTCCGGATGGATGACTTCACGGATGAATCCGGCCTCCAGAAGTCTCGCCACCTCCTC[G/A]
CGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGG
| 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 | 0.90% | 0.40% | 14.58% | 84.17% | NA |
| All Indica | 2759 | 0.10% | 0.30% | 7.00% | 92.57% | NA |
| All Japonica | 1512 | 2.30% | 0.00% | 24.40% | 73.28% | NA |
| Aus | 269 | 0.00% | 2.60% | 35.32% | 62.08% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.84% | 99.16% | NA |
| Indica II | 465 | 0.00% | 0.40% | 3.23% | 96.34% | NA |
| Indica III | 913 | 0.40% | 0.20% | 11.39% | 87.95% | NA |
| Indica Intermediate | 786 | 0.00% | 0.50% | 8.78% | 90.71% | NA |
| Temperate Japonica | 767 | 1.60% | 0.00% | 29.20% | 69.23% | NA |
| Tropical Japonica | 504 | 2.00% | 0.00% | 12.50% | 85.52% | NA |
| Japonica Intermediate | 241 | 5.40% | 0.00% | 34.02% | 60.58% | NA |
| VI/Aromatic | 96 | 1.00% | 2.10% | 14.58% | 82.29% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 20.00% | 77.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126364023 | C -> T | LOC_Os11g43670.1 | synonymous_variant ; p.Arg844Arg; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1126364023 | C -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |