Search for Variation information by Variation ID:
Detailed information for vg1218480248:
| Variant ID: vg1218480248 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480248 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGGAGAAAATACAAACCCCTAGGGGTAAAAGAAAAACGGAGAACCACTATAGCTGTACACTATACAGAGTGTGGGATTAACTCACGCAACCGCTTAGCTC[C/T]
TGCTAAAGCCCAAAGGCTCGCCTCCTCTTTGATTTTCATTAGTAGGAAGTTCGTTGCCACCTCTTTGTGATCAAAAATCCGCCGATTCCTCTCTTTCCAA
Reverse complement sequence
TTGGAAAGAGAGGAATCGGCGGATTTTTGATCACAAAGAGGTGGCAACGAACTTCCTACTAATGAAAATCAAAGAGGAGGCGAGCCTTTGGGCTTTAGCA[G/A]
GAGCTAAGCGGTTGCGTGAGTTAATCCCACACTCTGTATAGTGTACAGCTATAGTGGTTCTCCGTTTTTCTTTTACCCCTAGGGGTTTGTATTTTCTCCT
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 | 30.00% | 0.20% | 5.54% | 64.33% | NA |
| All Indica | 2759 | 14.20% | 0.00% | 6.78% | 79.05% | NA |
| All Japonica | 1512 | 42.90% | 0.50% | 4.23% | 52.31% | NA |
| Aus | 269 | 89.20% | 0.00% | 2.97% | 7.81% | NA |
| Indica I | 595 | 7.70% | 0.00% | 3.87% | 88.40% | NA |
| Indica II | 465 | 10.80% | 0.00% | 4.95% | 84.30% | NA |
| Indica III | 913 | 17.70% | 0.00% | 11.72% | 70.54% | NA |
| Indica Intermediate | 786 | 16.90% | 0.00% | 4.33% | 78.75% | NA |
| Temperate Japonica | 767 | 60.80% | 0.00% | 1.56% | 37.68% | NA |
| Tropical Japonica | 504 | 24.40% | 0.20% | 8.33% | 67.06% | NA |
| Japonica Intermediate | 241 | 24.90% | 2.90% | 4.15% | 68.05% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 2.22% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480248 | C -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:10.39; most accessible tissue: Callus, score: 21.903 | N | N | N | N |
| vg1218480248 | C -> T | LOC_Os12g30780.1 | missense_variant ; p.Gly255Arg; MODERATE | nonsynonymous_codon ; G255R | Average:10.39; most accessible tissue: Callus, score: 21.903 | probably damaging  |
2.607 |
TOLERATED | 0.05 |