Search for Variation information by Variation ID:
Detailed information for vg0817015809:
| Variant ID: vg0817015809 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015809 |
| Reference Allele: T | Alternative Allele: C,G |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTACCACAAGGTGTCAATGCTCAATTTCAGCCCCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGC[T/C,G]
GAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCA
Reverse complement sequence
TGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTC[A/G,C]
GCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGGGGCTGAAATTGAGCATTGACACCTTGTGGTAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.40% | 0.40% | 13.14% | 69.04% | G: 0.02% |
| All Indica | 2759 | 1.80% | 0.60% | 10.11% | 87.42% | NA |
| All Japonica | 1512 | 49.00% | 0.00% | 12.96% | 37.96% | G: 0.07% |
| Aus | 269 | 0.70% | 0.70% | 22.68% | 75.84% | NA |
| Indica I | 595 | 4.00% | 0.70% | 1.85% | 93.45% | NA |
| Indica II | 465 | 1.30% | 0.00% | 13.33% | 85.38% | NA |
| Indica III | 913 | 0.90% | 0.80% | 14.68% | 83.68% | NA |
| Indica Intermediate | 786 | 1.70% | 0.80% | 9.16% | 88.42% | NA |
| Temperate Japonica | 767 | 70.30% | 0.00% | 7.30% | 22.29% | G: 0.13% |
| Tropical Japonica | 504 | 19.60% | 0.00% | 18.06% | 62.30% | NA |
| Japonica Intermediate | 241 | 42.70% | 0.00% | 20.33% | 36.93% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 68.75% | 25.00% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 21.11% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015809 | T -> G | LOC_Os08g27910.1 | missense_variant ; p.Leu406Arg; MODERATE | nonsynonymous_codon ; L406R | Average:5.77; most accessible tissue: Callus, score: 12.96 | possibly damaging  |
1.925 |
TOLERATED | 0.33 |
| vg0817015809 | T -> C | LOC_Os08g27910.1 | missense_variant ; p.Leu406Pro; MODERATE | nonsynonymous_codon ; L406P | Average:5.77; most accessible tissue: Callus, score: 12.96 | probably damaging |
2.097 |
TOLERATED | 0.26 |
| vg0817015809 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.77; most accessible tissue: Callus, score: 12.96 | N | N | N | N |