Search for Variation information by Variation ID:
Detailed information for vg1007671423:
| Variant ID: vg1007671423 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671423 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 445. )
Flanking Sequence (100 bp) in Reference Genome:
TTTAGCTCTGTTACGAACGTACAACTTCAGAACTCCCATGTACCTTTCAAACGGCCACATTTCCCTTAGAAAAGCCGGGCCACATAGTTTTGTTTGCTTC[A/G]
CCAGATGAACAGGGAGATGAACCATTATATCAAAGAAAGACAGTGGGAAAAACATCTCCAGGTGACAGAGGGTATTCACAATATCGGTCTGCAGCCCATC
Reverse complement sequence
GATGGGCTGCAGACCGATATTGTGAATACCCTCTGTCACCTGGAGATGTTTTTCCCACTGTCTTTCTTTGATATAATGGTTCATCTCCCTGTTCATCTGG[T/C]
GAAGCAAACAAAACTATGTGGCCCGGCTTTTCTAAGGGAAATGTGGCCGTTTGAAAGGTACATGGGAGTTCTGAAGTTGTACGTTCGTAACAGAGCTAAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.80% | 0.30% | 10.73% | 75.18% | NA |
| All Indica | 2759 | 1.70% | 0.50% | 5.55% | 92.24% | NA |
| All Japonica | 1512 | 38.70% | 0.00% | 8.93% | 52.38% | NA |
| Aus | 269 | 0.70% | 0.00% | 68.77% | 30.48% | NA |
| Indica I | 595 | 0.80% | 0.30% | 1.01% | 97.82% | NA |
| Indica II | 465 | 1.50% | 0.60% | 7.74% | 90.11% | NA |
| Indica III | 913 | 1.90% | 0.80% | 5.59% | 91.79% | NA |
| Indica Intermediate | 786 | 2.30% | 0.30% | 7.63% | 89.82% | NA |
| Temperate Japonica | 767 | 53.50% | 0.00% | 7.56% | 38.98% | NA |
| Tropical Japonica | 504 | 8.70% | 0.00% | 9.92% | 81.35% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.00% | 11.20% | 34.44% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 25.00% | 72.92% | NA |
| Intermediate | 90 | 16.70% | 1.10% | 11.11% | 71.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671423 | A -> G | LOC_Os10g14130.1 | missense_variant ; p.Val273Ala; MODERATE | nonsynonymous_codon ; V273A | Average:6.735; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | benign  |
1.394 |
TOLERATED | 0.09 |
| vg1007671423 | A -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.735; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |