Search for Variation information by Variation ID:
Detailed information for vg0222980308:
| Variant ID: vg0222980308 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22980308 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
CTGTAAAGTTCAGTTTTATTTTCTTTCCATCTGTTAGTACTAGCTATTTTCATTGAATTTGCAGAATGTCCCAGATGCCATAGGCGGGCTCGAACACCTG[G/C]
AAGAGCTTCGCCTCGCTTCCAACGCGTTGGTCTCCCTCCCGGACTCCATAGGCCTCCTCACCAGCCTCAAGATCCTCGACGTCTCGGGCAACAAGCTGAG
Reverse complement sequence
CTCAGCTTGTTGCCCGAGACGTCGAGGATCTTGAGGCTGGTGAGGAGGCCTATGGAGTCCGGGAGGGAGACCAACGCGTTGGAAGCGAGGCGAAGCTCTT[C/G]
CAGGTGTTCGAGCCCGCCTATGGCATCTGGGACATTCTGCAAATTCAATGAAAATAGCTAGTACTAACAGATGGAAAGAAAATAAAACTGAACTTTACAG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.30% | 0.90% | 0.80% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 1.50% | 1.34% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.60% | 0.30% | 4.03% | 0.00% | NA |
| Indica II | 465 | 94.40% | 4.90% | 0.65% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.60% | 2.20% | 1.27% | 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 | 97.80% | 1.10% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0222980308 | G -> C | LOC_Os02g38040.1 | missense_variant ; p.Glu240Gln; MODERATE | nonsynonymous_codon ; E240Q | Average:72.722; most accessible tissue: Callus, score: 81.261 | possibly damaging  |
1.502 |
TOLERATED | 0.07 |