Search for Variation information by Variation ID:
Detailed information for vg1105161095:
| Variant ID: vg1105161095 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161095 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGG[T/C]
TGTGCGCCTTTGCTTGTTCAGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTTAGAAGAACACACGCAGAACCCCCTACC
Reverse complement sequence
GGTAGGGGGTTCTGCGTGTGTTCTTCTAAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCTGAACAAGCAAAGGCGCACA[A/G]
CCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.10% | 0.10% | 2.20% | 14.68% | NA |
| All Indica | 2759 | 77.10% | 0.00% | 2.97% | 19.97% | NA |
| All Japonica | 1512 | 91.70% | 0.10% | 1.19% | 6.94% | NA |
| Aus | 269 | 92.60% | 0.40% | 0.74% | 6.32% | NA |
| Indica I | 595 | 63.20% | 0.00% | 9.41% | 27.39% | NA |
| Indica II | 465 | 71.20% | 0.00% | 0.65% | 28.17% | NA |
| Indica III | 913 | 88.40% | 0.00% | 0.33% | 11.28% | NA |
| Indica Intermediate | 786 | 77.90% | 0.00% | 2.54% | 19.59% | NA |
| Temperate Japonica | 767 | 91.30% | 0.00% | 0.39% | 8.34% | NA |
| Tropical Japonica | 504 | 96.40% | 0.20% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 83.40% | 0.40% | 6.22% | 9.96% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 82.20% | 0.00% | 2.22% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161095 | T -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.02; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |
| vg1105161095 | T -> C | LOC_Os11g09660.1 | missense_variant ; p.Asn9Ser; MODERATE | nonsynonymous_codon | Average:6.02; most accessible tissue: Minghui63 root, score: 10.708 | benign  |
0.273 |
TOLERATED | 0.14 |