Search for Variation information by Variation ID:
Detailed information for vg0331481321:
| Variant ID: vg0331481321 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 31481321 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 327. )
Flanking Sequence (100 bp) in Reference Genome:
GCAACATTTTTGGATATGGAGAAGGATGGGATTGTGCCAGATATTGTTGTCTACAATGCACTTGTCTCTGCCTTCTGCAAAGCGAAAAAATTTGAGAATG[C/T]
CTTTAGAGTCCTTAATGATATGGAGGGCCATGGAATCACTACAAACTCAAGGACCTGGAACATCATCCTTAATCATCTGATTAGCCTTGGAAGGGATGAC
Reverse complement sequence
GTCATCCCTTCCAAGGCTAATCAGATGATTAAGGATGATGTTCCAGGTCCTTGAGTTTGTAGTGATTCCATGGCCCTCCATATCATTAAGGACTCTAAAG[G/A]
CATTCTCAAATTTTTTCGCTTTGCAGAAGGCAGAGACAAGTGCATTGTAGACAACAATATCTGGCACAATCCCATCCTTCTCCATATCCAAAAATGTTGC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.50% | 3.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 94.20% | 5.80% | 0.04% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.90% | 13.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 95.90% | 4.10% | 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 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0331481321 | C -> T | LOC_Os03g55340.1 | missense_variant ; p.Ala328Val; MODERATE | nonsynonymous_codon ; A328V | Average:73.17; most accessible tissue: Callus, score: 90.146 | benign  |
1.453 |
TOLERATED | 1.00 |