Search for Variation information by Variation ID:
Detailed information for vg1109584715:
| Variant ID: vg1109584715 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9584715 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )
Flanking Sequence (100 bp) in Reference Genome:
TTCAGCTGCACGATCTTTCCCGAAGTAAACTTCAGATCTACCGTGCCAACACCATGAACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAACCCC[G/A]
TGCGACCTGATAAGAAGAAAACAATGAGATGTCAGCACAAACATGTACATTGGCCCCAGTATCAACCCACCAATTAGTAGATTGATTAACTGAAAAAACA
Reverse complement sequence
TGTTTTTTCAGTTAATCAATCTACTAATTGGTGGGTTGATACTGGGGCCAATGTACATGTTTGTGCTGACATCTCATTGTTTTCTTCTTATCAGGTCGCA[C/T]
GGGGTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGTTCATGGTGTTGGCACGGTAGATCTGAAGTTTACTTCGGGAAAGATCGTGCAGCTGAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.60% | 4.40% | 25.14% | 11.87% | NA |
| All Indica | 2759 | 83.90% | 0.20% | 13.23% | 2.61% | NA |
| All Japonica | 1512 | 8.00% | 11.90% | 48.54% | 31.55% | NA |
| Aus | 269 | 95.90% | 0.40% | 1.49% | 2.23% | NA |
| Indica I | 595 | 81.80% | 0.00% | 10.25% | 7.90% | NA |
| Indica II | 465 | 80.60% | 0.40% | 17.20% | 1.72% | NA |
| Indica III | 913 | 89.50% | 0.10% | 9.97% | 0.44% | NA |
| Indica Intermediate | 786 | 81.00% | 0.40% | 16.92% | 1.65% | NA |
| Temperate Japonica | 767 | 5.90% | 0.40% | 44.07% | 49.67% | NA |
| Tropical Japonica | 504 | 10.10% | 32.30% | 48.21% | 9.33% | NA |
| Japonica Intermediate | 241 | 10.40% | 5.80% | 63.49% | 20.33% | NA |
| VI/Aromatic | 96 | 27.10% | 18.80% | 54.17% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 4.40% | 36.67% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109584715 | G -> A | LOC_Os11g17200.1 | missense_variant ; p.Arg324Trp; MODERATE | nonsynonymous_codon ; R324W | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
3.818 |
DELETERIOUS | 0.02 |
| vg1109584715 | G -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |