Search for Variation information by Variation ID:
Detailed information for vg0222980338:
| Variant ID: vg0222980338 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22980338 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 295. )
Flanking Sequence (100 bp) in Reference Genome:
CTGTTAGTACTAGCTATTTTCATTGAATTTGCAGAATGTCCCAGATGCCATAGGCGGGCTCGAACACCTGGAAGAGCTTCGCCTCGCTTCCAACGCGTTG[G/A]
TCTCCCTCCCGGACTCCATAGGCCTCCTCACCAGCCTCAAGATCCTCGACGTCTCGGGCAACAAGCTGAGGTCTCTCCCCGACAGCATCTCAAAATGCAG
Reverse complement sequence
CTGCATTTTGAGATGCTGTCGGGGAGAGACCTCAGCTTGTTGCCCGAGACGTCGAGGATCTTGAGGCTGGTGAGGAGGCCTATGGAGTCCGGGAGGGAGA[C/T]
CAACGCGTTGGAAGCGAGGCGAAGCTCTTCCAGGTGTTCGAGCCCGCCTATGGCATCTGGGACATTCTGCAAATTCAATGAAAATAGCTAGTACTAACAG
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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0222980338 | G -> A | LOC_Os02g38040.1 | missense_variant ; p.Val250Ile; MODERATE | nonsynonymous_codon ; V250I | Average:71.943; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | benign  |
0.289 |
TOLERATED | 0.11 |