Search for Variation information by Variation ID:
Detailed information for vg1105160997:
| Variant ID: vg1105160997 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160997 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCGTCGCCGTAGACGAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCTCGAGCGCCT[C/T]
CTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTG
Reverse complement sequence
CAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAG[G/A]
AGGCGCTCGAGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTCGTCTACGGCGACGG
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 | 64.00% | 0.30% | 9.14% | 26.60% | NA |
| All Indica | 2759 | 49.50% | 0.40% | 12.69% | 37.37% | NA |
| All Japonica | 1512 | 90.90% | 0.00% | 1.06% | 8.07% | NA |
| Aus | 269 | 54.30% | 0.00% | 21.93% | 23.79% | NA |
| Indica I | 595 | 32.40% | 0.00% | 8.24% | 59.33% | NA |
| Indica II | 465 | 44.10% | 0.40% | 10.32% | 45.16% | NA |
| Indica III | 913 | 61.10% | 1.10% | 17.20% | 20.59% | NA |
| Indica Intermediate | 786 | 52.20% | 0.00% | 12.21% | 35.62% | NA |
| Temperate Japonica | 767 | 90.90% | 0.00% | 0.13% | 9.00% | NA |
| Tropical Japonica | 504 | 94.80% | 0.00% | 0.60% | 4.56% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.00% | 4.98% | 12.45% | NA |
| VI/Aromatic | 96 | 81.20% | 0.00% | 3.12% | 15.62% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 4.44% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160997 | C -> T | LOC_Os11g09660.1 | missense_variant ; p.Glu42Lys; MODERATE | nonsynonymous_codon ; E42K | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
0.278 |
TOLERATED | 0.17 |
| vg1105160997 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |