Search for Variation information by Variation ID:
Detailed information for vg1109582515:
| Variant ID: vg1109582515 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9582515 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTACATCAACGAGCCAATGATTTGGGAGTATTCCAGTTGATTCCTAGCAATTCTCTTGTTCTTGCGAAGCAACAAGCTAGGATCATAAGGTGTTGGAGAA[G/A]
GTTTACTATCAATGTAGCCAAAACGATTCAAGATCTTCTCCACATAATGGGACTGCAAGAGTGTAATCCCATTCTCACCTCTAATTAGCTTAATGTTTAA
Reverse complement sequence
TTAAACATTAAGCTAATTAGAGGTGAGAATGGGATTACACTCTTGCAGTCCCATTATGTGGAGAAGATCTTGAATCGTTTTGGCTACATTGATAGTAAAC[C/T]
TTCTCCAACACCTTATGATCCTAGCTTGTTGCTTCGCAAGAACAAGAGAATTGCTAGGAATCAACTGGAATACTCCCAAATCATTGGCTCGTTGATGTAC
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 | 34.00% | 0.10% | 41.77% | 24.14% | NA |
| All Indica | 2759 | 3.70% | 0.00% | 60.46% | 35.88% | NA |
| All Japonica | 1512 | 95.40% | 0.30% | 2.12% | 2.18% | NA |
| Aus | 269 | 3.00% | 0.00% | 65.80% | 31.23% | NA |
| Indica I | 595 | 5.70% | 0.00% | 32.61% | 61.68% | NA |
| Indica II | 465 | 2.40% | 0.00% | 48.60% | 49.03% | NA |
| Indica III | 913 | 1.50% | 0.00% | 89.81% | 8.65% | NA |
| Indica Intermediate | 786 | 5.30% | 0.00% | 54.45% | 40.20% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 1.30% | 2.22% | NA |
| Tropical Japonica | 504 | 93.80% | 1.00% | 2.98% | 2.18% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 2.90% | 2.07% | NA |
| VI/Aromatic | 96 | 19.80% | 0.00% | 70.83% | 9.38% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 32.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1109582515 | G -> A | LOC_Os11g17200.1 | missense_variant ; p.Pro1057Leu; MODERATE | nonsynonymous_codon ; P1057L | Average:4.359; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.533 |
DELETERIOUS | 0.01 |
| vg1109582515 | G -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:4.359; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |