Search for Variation information by Variation ID:
Detailed information for vg0704649876:
| Variant ID: vg0704649876 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4649876 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 340. )
Flanking Sequence (100 bp) in Reference Genome:
CGTCATCACCACGCTTCCGCTGTCTTGACTCAACCATGGATCATGCCATGGTAAAGGACGATAACCTAAGGTCATCTCAGCTTTGTACCATGGAATTGCC[G/A]
CTCTCCAAGGTGATACTGGTGGAGAGCTACCTGTTTGCAGTAGTGTGAACTTGGAATTCACTTTAGTGAGCTCAACTAAATCCTCGGTGGCCATGTCATC
Reverse complement sequence
GATGACATGGCCACCGAGGATTTAGTTGAGCTCACTAAAGTGAATTCCAAGTTCACACTACTGCAAACAGGTAGCTCTCCACCAGTATCACCTTGGAGAG[C/T]
GGCAATTCCATGGTACAAAGCTGAGATGACCTTAGGTTATCGTCCTTTACCATGGCATGATCCATGGTTGAGTCAAGACAGCGGAAGCGTGGTGATGACG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 41.60% | 58.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.10% | 14.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704649876 | G -> A | LOC_Os07g08940.1 | missense_variant ; p.Ala227Val; MODERATE | nonsynonymous_codon ; A227V | Average:42.46; most accessible tissue: Zhenshan97 young leaf, score: 73.923 | benign  |
0.399 |
TOLERATED | 0.27 |