| Variant ID: vg1109584686 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9584686 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 340. )
TGTCGATAGAAGGGACATGCTGCACGTTCTTCAGCTGCACGATCTTTCCCGAAGTAAACTTCAGATCTACCGTGCCAACACCATGAACAGAAGCATGTGA[C/T]
CCATTCCCCATTAGGACGGTGGAACCCCGTGCGACCTGATAAGAAGAAAACAATGAGATGTCAGCACAAACATGTACATTGGCCCCAGTATCAACCCACC
GGTGGGTTGATACTGGGGCCAATGTACATGTTTGTGCTGACATCTCATTGTTTTCTTCTTATCAGGTCGCACGGGGTTCCACCGTCCTAATGGGGAATGG[G/A]
TCACATGCTTCTGTTCATGGTGTTGGCACGGTAGATCTGAAGTTTACTTCGGGAAAGATCGTGCAGCTGAAGAACGTGCAGCATGTCCCTTCTATCGACA
| 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 | 14.80% | 0.10% | 41.81% | 43.25% | NA |
| All Indica | 2759 | 1.70% | 0.00% | 58.64% | 39.62% | NA |
| All Japonica | 1512 | 36.40% | 0.00% | 9.39% | 54.17% | NA |
| Aus | 269 | 4.10% | 0.00% | 65.80% | 30.11% | NA |
| Indica I | 595 | 1.00% | 0.00% | 30.42% | 68.57% | NA |
| Indica II | 465 | 1.70% | 0.00% | 46.88% | 51.40% | NA |
| Indica III | 913 | 1.30% | 0.00% | 89.05% | 9.64% | NA |
| Indica Intermediate | 786 | 2.70% | 0.10% | 51.65% | 45.55% | NA |
| Temperate Japonica | 767 | 13.30% | 0.00% | 13.30% | 73.40% | NA |
| Tropical Japonica | 504 | 66.90% | 0.00% | 3.77% | 29.37% | NA |
| Japonica Intermediate | 241 | 46.50% | 0.00% | 8.71% | 44.81% | NA |
| VI/Aromatic | 96 | 71.90% | 3.10% | 10.42% | 14.58% | NA |
| Intermediate | 90 | 24.40% | 2.20% | 32.22% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109584686 | C -> T | LOC_Os11g17200.1 | synonymous_variant ; p.Gly333Gly; LOW | synonymous_codon | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1109584686 | C -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |