Search for Variation information by Variation ID:
Detailed information for vg0222935791:
| Variant ID: vg0222935791 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22935791 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 363. )
Flanking Sequence (100 bp) in Reference Genome:
GGACAATGTTGAGTTTACTCCGCAGCAAAGCCCACTACCTTGTCTTGTAAGCCCATCAGTAGAGCATGTATCCAACACATTACTCAATCCAAAGATCAAC[C/T]
ACCGATCGGACGCAATCTTCGGTGATCAGGTTAATCTAAGAGCAATTAAGTTTTGTCATAGTTGCATGAGTAACAAGTTCTTGTAGGAAGAATAAACTTT
Reverse complement sequence
AAAGTTTATTCTTCCTACAAGAACTTGTTACTCATGCAACTATGACAAAACTTAATTGCTCTTAGATTAACCTGATCACCGAAGATTGCGTCCGATCGGT[G/A]
GTTGATCTTTGGATTGAGTAATGTGTTGGATACATGCTCTACTGATGGGCTTACAAGACAAGGTAGTGGGCTTTGCTGCGGAGTAAACTCAACATTGTCC
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 | 96.20% | 2.30% | 1.52% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.00% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 88.60% | 7.10% | 4.30% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 83.70% | 9.60% | 6.65% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 82.20% | 14.10% | 3.73% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0222935791 | C -> T | LOC_Os02g37950.1 | missense_variant ; p.His79Tyr; MODERATE | nonsynonymous_codon ; H79Y | Average:66.985; most accessible tissue: Minghui63 young leaf, score: 78.443 | benign  |
0.833 |
DELETERIOUS | 0.01 |
| vg0222935791 | C -> T | LOC_Os02g37950.2 | missense_variant ; p.His79Tyr; MODERATE | nonsynonymous_codon ; H79Y | Average:66.985; most accessible tissue: Minghui63 young leaf, score: 78.443 | benign |
0.833 |
DELETERIOUS | 0.01 |
| vg0222935791 | C -> T | LOC_Os02g37950.3 | missense_variant ; p.His79Tyr; MODERATE | nonsynonymous_codon ; H79Y | Average:66.985; most accessible tissue: Minghui63 young leaf, score: 78.443 | benign |
0.833 |
DELETERIOUS | 0.01 |