Search for Variation information by Variation ID:
Detailed information for vg0318608191:
| Variant ID: vg0318608191 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608191 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.29, others allele: 0.00, population size: 72. )
Flanking Sequence (100 bp) in Reference Genome:
TTCTCCGACACCATCTCCCGGAAATCATCAAGCACGGCCATGGACACCTTGTGGAACCCCTCCGACTCGGTGCACGACGCCACAATCCCCTTCTGCCAGT[T/C]
CTGCCCAGCCTCTGCCCACACAGAAACGCAAGGGAGAGAAAAACAACACACACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCA
Reverse complement sequence
TGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGCGTTTCTGTGTGGGCAGAGGCTGGGCAG[A/G]
ACTGGCAGAAGGGGATTGTGGCGTCGTGCACCGAGTCGGAGGGGTTCCACAAGGTGTCCATGGCCGTGCTTGATGATTTCCGGGAGATGGTGTCGGAGAA
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 | 34.50% | 0.20% | 34.15% | 31.17% | NA |
| All Indica | 2759 | 5.40% | 0.10% | 52.30% | 42.23% | NA |
| All Japonica | 1512 | 86.30% | 0.10% | 1.06% | 12.50% | NA |
| Aus | 269 | 19.00% | 0.40% | 43.49% | 37.17% | NA |
| Indica I | 595 | 5.50% | 0.00% | 39.83% | 54.62% | NA |
| Indica II | 465 | 3.90% | 0.00% | 56.77% | 39.35% | NA |
| Indica III | 913 | 3.50% | 0.10% | 62.76% | 33.63% | NA |
| Indica Intermediate | 786 | 8.30% | 0.30% | 46.95% | 44.53% | NA |
| Temperate Japonica | 767 | 99.60% | 0.10% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 66.50% | 0.00% | 2.18% | 31.35% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.40% | 1.66% | 12.45% | NA |
| VI/Aromatic | 96 | 80.20% | 2.10% | 16.67% | 1.04% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 24.44% | 20.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608191 | T -> C | LOC_Os03g32526.1 | missense_variant ; p.Asn99Asp; MODERATE | nonsynonymous_codon | Average:18.95; most accessible tissue: Zhenshan97 panicle, score: 39.652 | possibly damaging  |
-1.819 |
TOLERATED | 0.85 |
| vg0318608191 | T -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:18.95; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |