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Detailed information for vg1202830986:
| Variant ID: vg1202830986 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2830986 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
TGCAGTTATTGTTAAGCATGGTTTTCATAGGAACCTCTTTGTAGCAACATCTCTTGTGGATGTCTATGCAAAGTGTGGTCAGATTGAAAAATCATATGAA[G/A]
TATTTGCTGATATGGAAGAAAAGAATGTTGTCTTATGGAATGCAATGATTGCTAGTTTTTCTAGGCATGCTCATTCTTGGGAAGCAATGATTCTCTTTGA
Reverse complement sequence
TCAAAGAGAATCATTGCTTCCCAAGAATGAGCATGCCTAGAAAAACTAGCAATCATTGCATTCCATAAGACAACATTCTTTTCTTCCATATCAGCAAATA[C/T]
TTCATATGATTTTTCAATCTGACCACACTTTGCATAGACATCCACAAGAGATGTTGCTACAAAGAGGTTCCTATGAAAACCATGCTTAACAATAACTGCA
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 | 95.10% | 4.90% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.70% | 4.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 60.60% | 39.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202830986 | G -> A | LOC_Os12g06070.1 | missense_variant ; p.Val315Ile; MODERATE | nonsynonymous_codon ; V315I | Average:49.372; most accessible tissue: Callus, score: 84.964 | benign  |
0.316 |
TOLERATED | 0.37 |