Search for Variation information by Variation ID:
Detailed information for vg1109582115:
| Variant ID: vg1109582115 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9582115 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAGCCGGCACCGGTTTTTCAACAACAGGCAGATCCATTAATAGATCACGCAGCCATTCAGCCTCAACAGTAGCAGTATCCAGTGCCGTTAGCTCTGCTTC[C/T]
ATTGTTGACCTCGTCAAAATGGTCTGTTTGCAAGACCTCCATGAAACAGCACCACCACCCAGTGTGAAAACATATCCACTAGTGGCTTTGATCTCATCCA
Reverse complement sequence
TGGATGAGATCAAAGCCACTAGTGGATATGTTTTCACACTGGGTGGTGGTGCTGTTTCATGGAGGTCTTGCAAACAGACCATTTTGACGAGGTCAACAAT[G/A]
GAAGCAGAGCTAACGGCACTGGATACTGCTACTGTTGAGGCTGAATGGCTGCGTGATCTATTAATGGATCTGCCTGTTGTTGAAAAACCGGTGCCGGCTA
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 | 33.80% | 0.20% | 40.90% | 25.07% | NA |
| All Indica | 2759 | 3.60% | 0.00% | 59.04% | 37.33% | NA |
| All Japonica | 1512 | 95.00% | 0.70% | 1.98% | 2.38% | NA |
| Aus | 269 | 3.00% | 0.00% | 66.17% | 30.86% | NA |
| Indica I | 595 | 5.40% | 0.00% | 29.58% | 65.04% | NA |
| Indica II | 465 | 3.00% | 0.00% | 46.45% | 50.54% | NA |
| Indica III | 913 | 1.60% | 0.00% | 89.49% | 8.87% | NA |
| Indica Intermediate | 786 | 5.00% | 0.00% | 53.44% | 41.60% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 1.30% | 2.22% | NA |
| Tropical Japonica | 504 | 92.70% | 2.00% | 2.58% | 2.78% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 2.90% | 2.07% | NA |
| VI/Aromatic | 96 | 18.80% | 0.00% | 71.88% | 9.38% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 30.00% | 30.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109582115 | C -> T | LOC_Os11g17200.1 | missense_variant ; p.Met1190Ile; MODERATE | nonsynonymous_codon ; M1190I | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | benign  |
0.596 |
DELETERIOUS | 0.04 |
| vg1109582115 | C -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |