Search for Variation information by Variation ID:
Detailed information for vg0905621375:
| Variant ID: vg0905621375 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5621375 |
| 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: 313. )
Flanking Sequence (100 bp) in Reference Genome:
CGATGACGAAGCTCTCCAATGGCCACCAAAGCTGCCTCCTGACAAGCATGAATATAATCTCTTCCTCCAGCTTCAAACATCATTGATGGAAGGTCTTCAC[G/A]
ATCACTAGTCAACGTCATGCGAACACGACTATTCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAATGTTGTAGCCTACTTCAAATGCC
Reverse complement sequence
GGCATTTGAAGTAGGCTACAACATTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGAATAGTCGTGTTCGCATGACGTTGACTAGTGAT[C/T]
GTGAAGACCTTCCATCAATGATGTTTGAAGCTGGAGGAAGAGATTATATTCATGCTTGTCAGGAGGCAGCTTTGGTGGCCATTGGAGAGCTTCGTCATCG
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 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 82.30% | 17.70% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 82.70% | 17.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 54.80% | 45.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905621375 | G -> A | LOC_Os09g10310.1 | missense_variant ; p.Arg52Cys; MODERATE | nonsynonymous_codon ; R52C | Average:42.905; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | probably damaging  |
3.16 |
TOLERATED | 0.08 |