Search for Variation information by Variation ID:
Detailed information for vg0334098463:
| Variant ID: vg0334098463 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098463 |
| 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: 350. )
Flanking Sequence (100 bp) in Reference Genome:
GTGTTCTCATTATGAACAGTTCCGTATTAGTTCAATACTTTCCTGATATAACTAATCATAACTATTATCTTCTTGCAGCCGAAGTGGGTTAGCGGGACGA[C/T]
GCGTCGTGTGTACACACAGTTCGTAGCTGATTTTGATCAGCTTACGTCTAACCGTGTTCGGTGGACTCCCTACACTCAGCACGATGACAATGATCGTGCA
Reverse complement sequence
TGCACGATCATTGTCATCGTGCTGAGTGTAGGGAGTCCACCGAACACGGTTAGACGTAAGCTGATCAAAATCAGCTACGAACTGTGTGTACACACGACGC[G/A]
TCGTCCCGCTAACCCACTTCGGCTGCAAGAAGATAATAGTTATGATTAGTTATATCAGGAAAGTATTGAACTAATACGGAACTGTTCATAATGAGAACAC
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 | 96.10% | 3.90% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 93.40% | 6.60% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 82.20% | 17.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.30% | 3.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098463 | C -> T | LOC_Os03g59910.1 | missense_variant ; p.Thr31Met; MODERATE | nonsynonymous_codon ; T31M | Average:50.814; most accessible tissue: Callus, score: 68.635 | probably damaging  |
2.771 |
DELETERIOUS | 0.01 |