Search for Variation information by Variation ID:
Detailed information for vg1109584726:
| Variant ID: vg1109584726 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9584726 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
GATCTTTCCCGAAGTAAACTTCAGATCTACCGTGCCAACACCATGAACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAACCCCGTGCGACCTGA[T/C]
AAGAAGAAAACAATGAGATGTCAGCACAAACATGTACATTGGCCCCAGTATCAACCCACCAATTAGTAGATTGATTAACTGAAAAAACAGTAGGTAAATT
Reverse complement sequence
AATTTACCTACTGTTTTTTCAGTTAATCAATCTACTAATTGGTGGGTTGATACTGGGGCCAATGTACATGTTTGTGCTGACATCTCATTGTTTTCTTCTT[A/G]
TCAGGTCGCACGGGGTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGTTCATGGTGTTGGCACGGTAGATCTGAAGTTTACTTCGGGAAAGATC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.20% | 1.20% | 56.69% | 27.93% | NA |
| All Indica | 2759 | 3.70% | 1.60% | 81.15% | 13.59% | NA |
| All Japonica | 1512 | 28.40% | 0.30% | 11.57% | 59.72% | NA |
| Aus | 269 | 16.00% | 1.50% | 79.93% | 2.60% | NA |
| Indica I | 595 | 1.20% | 0.80% | 62.02% | 35.97% | NA |
| Indica II | 465 | 5.60% | 0.90% | 81.51% | 12.04% | NA |
| Indica III | 913 | 2.80% | 2.80% | 93.21% | 1.10% | NA |
| Indica Intermediate | 786 | 5.50% | 1.00% | 81.42% | 12.09% | NA |
| Temperate Japonica | 767 | 6.50% | 0.50% | 8.34% | 84.62% | NA |
| Tropical Japonica | 504 | 63.30% | 0.20% | 10.32% | 26.19% | NA |
| Japonica Intermediate | 241 | 24.90% | 0.00% | 24.48% | 50.62% | NA |
| VI/Aromatic | 96 | 77.10% | 1.00% | 15.62% | 6.25% | NA |
| Intermediate | 90 | 26.70% | 2.20% | 38.89% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109584726 | T -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1109584726 | T -> C | LOC_Os11g17200.1 | missense_variant ; p.Tyr320Cys; MODERATE | nonsynonymous_codon ; Y320C | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
3.316 |
DELETERIOUS | 0.00 |