Search for Variation information by Variation ID:
Detailed information for vg0424400923:
| Variant ID: vg0424400923 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24400923 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, C: 0.02, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
TAGCCTGAGGTACCTGCTTAGCTTTGAGGTAAGCATGAATAAGTGCAGTATATGTCACCACAGTTGGGGAGCAACCCACACTCCTCATCTCCTCAAACAA[C/A]
CACTGGGCTTGTTCAATGAGTCCAGCTTTACAAAAGCTGTCAATCAAAATTGTGTATGTATACACATCAGGAGTTACACCGACCATCTTCATCTCTTGGA
Reverse complement sequence
TCCAAGAGATGAAGATGGTCGGTGTAACTCCTGATGTGTATACATACACAATTTTGATTGACAGCTTTTGTAAAGCTGGACTCATTGAACAAGCCCAGTG[G/T]
TTGTTTGAGGAGATGAGGAGTGTGGGTTGCTCCCCAACTGTGGTGACATATACTGCACTTATTCATGCTTACCTCAAAGCTAAGCAGGTACCTCAGGCTA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.30% | 24.60% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 62.70% | 37.20% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 55.80% | 44.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 73.60% | 26.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.30% | 4.50% | 0.22% | 0.00% | NA |
| Indica III | 913 | 42.10% | 57.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 59.30% | 40.50% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 16.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424400923 | C -> A | LOC_Os04g41140.1 | missense_variant ; p.Trp513Cys; MODERATE | nonsynonymous_codon ; W513C | Average:58.683; most accessible tissue: Zhenshan97 young leaf, score: 77.736 | probably damaging  |
3.238 |
TOLERATED | 0.11 |