Search for Variation information by Variation ID:
Detailed information for vg1107678757:
| Variant ID: vg1107678757 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7678757 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TACTATAGCACAGCTGATAAAGGTGGCATTTAAAGGACATCTATTGTTATCTTGACGTTGGGTGGCTTGTAGAAGTGAAAGATGCAAACTGAATGGAGAT[G/A]
AATGGCATTGGTTGCTGCAAAAGTTGCCCATCCTCTCTTTAGGTTGCAACGATCGTCCGATGATTTATGCAGGAGCATGGTGACTGAATCACTGCCTGCT
Reverse complement sequence
AGCAGGCAGTGATTCAGTCACCATGCTCCTGCATAAATCATCGGACGATCGTTGCAACCTAAAGAGAGGATGGGCAACTTTTGCAGCAACCAATGCCATT[C/T]
ATCTCCATTCAGTTTGCATCTTTCACTTCTACAAGCCACCCAACGTCAAGATAACAATAGATGTCCTTTAAATGCCACCTTTATCAGCTGTGCTATAGTA
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 | 41.60% | 0.10% | 7.41% | 50.85% | NA |
| All Indica | 2759 | 6.50% | 0.00% | 10.62% | 82.89% | NA |
| All Japonica | 1512 | 93.00% | 0.00% | 2.71% | 4.30% | NA |
| Aus | 269 | 88.80% | 1.90% | 2.97% | 6.32% | NA |
| Indica I | 595 | 5.20% | 0.00% | 7.73% | 87.06% | NA |
| Indica II | 465 | 2.20% | 0.00% | 6.88% | 90.97% | NA |
| Indica III | 913 | 3.90% | 0.00% | 13.69% | 82.37% | NA |
| Indica Intermediate | 786 | 13.00% | 0.00% | 11.45% | 75.57% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.78% | 2.61% | NA |
| Tropical Japonica | 504 | 92.30% | 0.00% | 4.76% | 2.98% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 4.56% | 12.45% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 8.89% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107678757 | G -> A | LOC_Os11g13900.1 | missense_variant ; p.His210Tyr; MODERATE | nonsynonymous_codon ; H210Y | Average:5.775; most accessible tissue: Callus, score: 18.856 | benign  |
1.317 |
TOLERATED | 0.31 |
| vg1107678757 | G -> DEL | LOC_Os11g13900.1 | N | frameshift_variant | Average:5.775; most accessible tissue: Callus, score: 18.856 | N | N | N | N |