Search for Variation information by Variation ID:
Detailed information for vg0807401447:
| Variant ID: vg0807401447 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7401447 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCCGCCAAGAACTATGTACGTCACAGCGGTTGGGTTGTGCGGGATAACGTGCCTGTCAGTACGGTGTACTGGCGAAGAACAAGGTTACGCGGAGATCAT[G/C]
AGAGCTTTGTCCCAGATTCGGAGAAAGAGATGCTGTGGACCACAATGCTCGAGACATTCACCCTTCCTGCGGGTACAGAGGACAAAGTGAAAAGGTGGAC
Reverse complement sequence
GTCCACCTTTTCACTTTGTCCTCTGTACCCGCAGGAAGGGTGAATGTCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCCGAATCTGGGACAAAGCTCT[C/G]
ATGATCTCCGCGTAACCTTGTTCTTCGCCAGTACACCGTACTGACAGGCACGTTATCCCGCACAACCCAACCGCTGTGACGTACATAGTTCTTGGCGGCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.40% | 0.70% | 5.63% | 54.21% | NA |
| All Indica | 2759 | 17.00% | 0.00% | 6.96% | 76.01% | NA |
| All Japonica | 1512 | 88.20% | 2.20% | 2.51% | 7.01% | NA |
| Aus | 269 | 4.10% | 0.00% | 8.92% | 86.99% | NA |
| Indica I | 595 | 39.80% | 0.00% | 5.71% | 54.45% | NA |
| Indica II | 465 | 17.20% | 0.00% | 9.68% | 73.12% | NA |
| Indica III | 913 | 2.30% | 0.10% | 4.60% | 92.99% | NA |
| Indica Intermediate | 786 | 16.70% | 0.00% | 9.03% | 74.30% | NA |
| Temperate Japonica | 767 | 86.70% | 0.00% | 1.96% | 11.34% | NA |
| Tropical Japonica | 504 | 94.40% | 1.60% | 1.79% | 2.18% | NA |
| Japonica Intermediate | 241 | 80.10% | 10.80% | 5.81% | 3.32% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 6.25% | 86.46% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 6.67% | 46.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807401447 | G -> C | LOC_Os08g12500.1 | missense_variant ; p.Glu1088Gln; MODERATE | nonsynonymous_codon ; E1088Q | Average:7.184; most accessible tissue: Zhenshan97 root, score: 10.511 | possibly damaging  |
1.502 |
DELETERIOUS | 0.00 |
| vg0807401447 | G -> DEL | LOC_Os08g12500.1 | N | frameshift_variant | Average:7.184; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |