Search for Variation information by Variation ID:
Detailed information for vg0137499921:
| Variant ID: vg0137499921 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37499921 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 58. )
Flanking Sequence (100 bp) in Reference Genome:
AGAAGCACGACCCCCTCTCGGGGTAGATTGTTCCCCCCTGCGGCTCCCGCCTGCGCCGTCGTGGCCCTTTGGAGCTCGCTCCTCTGAGGCCCCGACCGCC[A/G]
TCATAATGGTCAGGATGGAGGCGCGGTCTGGATCGCTGCAGAGGGGGAGGATTCCTTGGGGAATGAGGGCCGCCTCTACGGAGTTGAGATTCAGCACCCG
Reverse complement sequence
CGGGTGCTGAATCTCAACTCCGTAGAGGCGGCCCTCATTCCCCAAGGAATCCTCCCCCTCTGCAGCGATCCAGACCGCGCCTCCATCCTGACCATTATGA[T/C]
GGCGGTCGGGGCCTCAGAGGAGCGAGCTCCAAAGGGCCACGACGGCGCAGGCGGGAGCCGCAGGGGGGAACAATCTACCCCGAGAGGGGGTCGTGCTTCT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.80% | 0.10% | 6.24% | 65.85% | NA |
| All Indica | 2759 | 1.80% | 0.20% | 0.22% | 97.72% | NA |
| All Japonica | 1512 | 74.30% | 0.00% | 18.45% | 7.21% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 0.30% | 0.30% | 0.17% | 99.16% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.00% | 98.92% | NA |
| Indica III | 913 | 0.70% | 0.20% | 0.33% | 98.80% | NA |
| Indica Intermediate | 786 | 4.80% | 0.30% | 0.25% | 94.66% | NA |
| Temperate Japonica | 767 | 72.40% | 0.00% | 20.47% | 7.17% | NA |
| Tropical Japonica | 504 | 87.30% | 0.00% | 7.54% | 5.16% | NA |
| Japonica Intermediate | 241 | 53.50% | 0.00% | 34.85% | 11.62% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 6.25% | 5.21% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 4.44% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137499921 | A -> G | LOC_Os01g64610.1 | missense_variant ; p.Met266Thr; MODERATE | nonsynonymous_codon ; M266T | Average:4.834; most accessible tissue: Callus, score: 8.507 | benign  |
-0.051 |
TOLERATED | 0.38 |
| vg0137499921 | A -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:4.834; most accessible tissue: Callus, score: 8.507 | N | N | N | N |