Search for Variation information by Variation ID:
Detailed information for vg0135359483:
| Variant ID: vg0135359483 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35359483 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
TCAAAGCCAATGTTACCAACAACACTGCTGTACATCTCACTTGCCACAAAAGCTGAAGTGATGTTTCGGTGATACTTCTCCACCCCTTGTAAGTAGCACT[T/G]
GTGCTCGGTCACAATACTAACTTTCCAATAATCATTCCATTTACCCTTATATGCATGGACACGCCACGGACAATCTTCCTTCATGCATCTCACTTCATAC
Reverse complement sequence
GTATGAAGTGAGATGCATGAAGGAAGATTGTCCGTGGCGTGTCCATGCATATAAGGGTAAATGGAATGATTATTGGAAAGTTAGTATTGTGACCGAGCAC[A/C]
AGTGCTACTTACAAGGGGTGGAGAAGTATCACCGAAACATCACTTCAGCTTTTGTGGCAAGTGAGATGTACAGCAGTGTTGTTGGTAACATTGGCTTTGA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.60% | 1.10% | 3.15% | 71.22% | NA |
| All Indica | 2759 | 3.20% | 1.80% | 2.50% | 92.53% | NA |
| All Japonica | 1512 | 62.10% | 0.00% | 4.89% | 33.00% | NA |
| Aus | 269 | 1.90% | 0.00% | 0.37% | 97.77% | NA |
| Indica I | 595 | 4.50% | 0.80% | 1.51% | 93.11% | NA |
| Indica II | 465 | 0.60% | 4.10% | 2.37% | 92.90% | NA |
| Indica III | 913 | 2.20% | 2.20% | 4.16% | 91.46% | NA |
| Indica Intermediate | 786 | 4.70% | 0.80% | 1.40% | 93.13% | NA |
| Temperate Japonica | 767 | 54.80% | 0.00% | 0.39% | 44.85% | NA |
| Tropical Japonica | 504 | 63.90% | 0.00% | 13.89% | 22.22% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.41% | 17.84% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 5.56% | 48.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135359483 | T -> G | LOC_Os01g61090.1 | missense_variant ; p.Lys288Gln; MODERATE | nonsynonymous_codon ; K288Q | Average:10.981; most accessible tissue: Zhenshan97 panicle, score: 32.308 | benign  |
0.492 |
TOLERATED | 0.21 |
| vg0135359483 | T -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:10.981; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |