Search for Variation information by Variation ID:
Detailed information for vg0141809216:
| Variant ID: vg0141809216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41809216 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, G: 0.22, A: 0.12, others allele: 0.00, population size: 50. )
Flanking Sequence (100 bp) in Reference Genome:
GGCCCCTGTGAGCCCCAGGGATCGCAGGCCCGCCAGGCGGTCGAGGACGGCGTCATAGCCATCTCCCAGATCTACCGGCGCCCGCCAGCTGGAGGCCTGC[C/A]
CCGGGGGCTGGCTCGGAAGTCGGAGGCGCGCTTCGTCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCATCCCACTTCTTGCGGAGGACGCAGGG
Reverse complement sequence
CCCTGCGTCCTCCGCAAGAAGTGGGATGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGACGAAGCGCGCCTCCGACTTCCGAGCCAGCCCCCGG[G/T]
GCAGGCCTCCAGCTGGCGGGCGCCGGTAGATCTGGGAGATGGCTATGACGCCGTCCTCGACCGCCTGGCGGGCCTGCGATCCCTGGGGCTCACAGGGGCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.10% | 1.80% | 3.22% | 76.89% | NA |
| All Indica | 2759 | 2.40% | 3.00% | 5.36% | 89.27% | NA |
| All Japonica | 1512 | 43.80% | 0.00% | 0.00% | 56.22% | NA |
| Aus | 269 | 34.90% | 0.00% | 0.37% | 64.68% | NA |
| Indica I | 595 | 3.70% | 2.40% | 6.22% | 87.73% | NA |
| Indica II | 465 | 1.30% | 2.20% | 2.15% | 94.41% | NA |
| Indica III | 913 | 1.00% | 5.00% | 6.90% | 87.08% | NA |
| Indica Intermediate | 786 | 3.60% | 1.70% | 4.83% | 89.95% | NA |
| Temperate Japonica | 767 | 76.90% | 0.00% | 0.00% | 23.08% | NA |
| Tropical Japonica | 504 | 4.60% | 0.00% | 0.00% | 95.44% | NA |
| Japonica Intermediate | 241 | 20.30% | 0.00% | 0.00% | 79.67% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 0.00% | 85.42% | NA |
| Intermediate | 90 | 23.30% | 1.10% | 3.33% | 72.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141809216 | C -> A | LOC_Os01g72070.1 | missense_variant ; p.Gly119Val; MODERATE | nonsynonymous_codon ; G119V | Average:5.279; most accessible tissue: Callus, score: 13.399 | benign  |
-0.91 |
TOLERATED | 0.07 |
| vg0141809216 | C -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:5.279; most accessible tissue: Callus, score: 13.399 | N | N | N | N |