Search for Variation information by Variation ID:
Detailed information for vg1105160339:
| Variant ID: vg1105160339 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160339 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGCGGGTGGCAAGTTCATTAGCCAACCCCGTGCCTGTCCCTTCAGGGCCATGGGAAAGAAATTCGCCATGACCCTGTCGTCACCCCCGGCGGCCTCGATC[C/T]
CGGTCGTGTAGACTTGGAGAAACTCGGCGGGGTTGACGCTCCCGTCATATTTTTCGGCGATGGTGGGCCGGAACCTTGGGGGCCAACGGACGTTCCGAAG
Reverse complement sequence
CTTCGGAACGTCCGTTGGCCCCCAAGGTTCCGGCCCACCATCGCCGAAAAATATGACGGGAGCGTCAACCCCGCCGAGTTTCTCCAAGTCTACACGACCG[G/A]
GATCGAGGCCGCCGGGGGTGACGACAGGGTCATGGCGAATTTCTTTCCCATGGCCCTGAAGGGACAGGCACGGGGTTGGCTAATGAACTTGCCACCCGCG
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 | 9.90% | 0.60% | 24.23% | 65.28% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 21.93% | 76.98% | NA |
| All Japonica | 1512 | 27.80% | 1.70% | 24.67% | 45.90% | NA |
| Aus | 269 | 0.70% | 0.00% | 29.37% | 69.89% | NA |
| Indica I | 595 | 2.40% | 0.00% | 12.61% | 85.04% | NA |
| Indica II | 465 | 0.40% | 0.00% | 8.39% | 91.18% | NA |
| Indica III | 913 | 0.10% | 0.00% | 32.31% | 67.58% | NA |
| Indica Intermediate | 786 | 1.50% | 0.10% | 24.94% | 73.41% | NA |
| Temperate Japonica | 767 | 34.00% | 0.70% | 11.08% | 54.24% | NA |
| Tropical Japonica | 504 | 14.10% | 0.00% | 48.02% | 37.90% | NA |
| Japonica Intermediate | 241 | 36.50% | 8.30% | 19.09% | 36.10% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 67.71% | 27.08% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 25.56% | 58.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160339 | C -> T | LOC_Os11g09660.1 | missense_variant ; p.Gly261Glu; MODERATE | nonsynonymous_codon ; G261E | Average:7.966; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.783 |
DELETERIOUS | 0.00 |
| vg1105160339 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:7.966; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |