Search for Variation information by Variation ID:
Detailed information for vg1109584718:
| Variant ID: vg1109584718 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9584718 |
| 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: 295. )
Flanking Sequence (100 bp) in Reference Genome:
AGCTGCACGATCTTTCCCGAAGTAAACTTCAGATCTACCGTGCCAACACCATGAACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAACCCCGTG[C/T]
GACCTGATAAGAAGAAAACAATGAGATGTCAGCACAAACATGTACATTGGCCCCAGTATCAACCCACCAATTAGTAGATTGATTAACTGAAAAAACAGTA
Reverse complement sequence
TACTGTTTTTTCAGTTAATCAATCTACTAATTGGTGGGTTGATACTGGGGCCAATGTACATGTTTGTGCTGACATCTCATTGTTTTCTTCTTATCAGGTC[G/A]
CACGGGGTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGTTCATGGTGTTGGCACGGTAGATCTGAAGTTTACTTCGGGAAAGATCGTGCAGCT
Allele Frequencies:
| 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 | 51.90% | 0.30% | 17.77% | 29.96% | NA |
| All Indica | 2759 | 59.80% | 0.10% | 21.06% | 19.06% | NA |
| All Japonica | 1512 | 41.90% | 0.50% | 5.16% | 52.45% | NA |
| Aus | 269 | 16.40% | 1.90% | 57.62% | 24.16% | NA |
| Indica I | 595 | 33.40% | 0.00% | 24.20% | 42.35% | NA |
| Indica II | 465 | 48.20% | 0.00% | 34.84% | 16.99% | NA |
| Indica III | 913 | 85.30% | 0.00% | 11.17% | 3.50% | NA |
| Indica Intermediate | 786 | 56.90% | 0.40% | 22.01% | 20.74% | NA |
| Temperate Japonica | 767 | 22.30% | 0.00% | 5.87% | 71.84% | NA |
| Tropical Japonica | 504 | 65.90% | 1.40% | 4.56% | 28.17% | NA |
| Japonica Intermediate | 241 | 53.90% | 0.40% | 4.15% | 41.49% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 6.25% | 10.42% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 22.22% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109584718 | C -> T | LOC_Os11g17200.1 | missense_variant ; p.Ala323Thr; MODERATE | nonsynonymous_codon ; A323T | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.885 |
DELETERIOUS | 0.03 |
| vg1109584718 | C -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |