Search for Variation information by Variation ID:
Detailed information for vg1109410736:
| Variant ID: vg1109410736 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9410736 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGCTGACGCCGGTGAGACGATATCGCTCGAGATTATCCATTATTCGTCATGAACAATGGCACACACGGCCTCCCAGCTCTCCCGGTAGAGCTGCCTCCGC[G/A]
TCTCGGCGTGCACCTTCCCGTCCTCGCCAGCCGCCGGCCACTCGCCGACGAGCCTCTCCGCCTCCCGCACCACGCCGTCGCGGCTGGCCGCCTCGCCGTC
Reverse complement sequence
GACGGCGAGGCGGCCAGCCGCGACGGCGTGGTGCGGGAGGCGGAGAGGCTCGTCGGCGAGTGGCCGGCGGCTGGCGAGGACGGGAAGGTGCACGCCGAGA[C/T]
GCGGAGGCAGCTCTACCGGGAGAGCTGGGAGGCCGTGTGTGCCATTGTTCATGACGAATAATGGATAATCTCGAGCGATATCGTCTCACCGGCGTCAGCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.80% | 39.60% | 0.02% | 0.63% | NA |
| All Indica | 2759 | 95.10% | 4.30% | 0.04% | 0.58% | NA |
| All Japonica | 1512 | 3.70% | 95.70% | 0.00% | 0.60% | NA |
| Aus | 269 | 9.30% | 90.30% | 0.00% | 0.37% | NA |
| Indica I | 595 | 93.60% | 3.70% | 0.00% | 2.69% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.60% | 8.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 3.40% | 96.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 3.60% | 94.60% | 0.00% | 1.79% | NA |
| Japonica Intermediate | 241 | 5.00% | 95.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 71.90% | 28.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 38.90% | 0.00% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109410736 | G -> A | LOC_Os11g16970.1 | missense_variant ; p.Thr231Met; MODERATE | nonsynonymous_codon ; T231M | Average:73.375; most accessible tissue: Zhenshan97 young leaf, score: 89.339 | benign  |
0.418 |
TOLERATED | 1.00 |
| vg1109410736 | G -> DEL | LOC_Os11g16970.1 | N | frameshift_variant | Average:73.375; most accessible tissue: Zhenshan97 young leaf, score: 89.339 | N | N | N | N |