Search for Variation information by Variation ID:
Detailed information for vg0143001308:
| Variant ID: vg0143001308 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001308 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.82, C: 0.19, others allele: 0.00, population size: 159. )
Flanking Sequence (100 bp) in Reference Genome:
GCCGTCGCCCAGGGCAACCTCCTTGACCGGGACCTCGTCGCCTGTGATCATCCGCTGCCTCGGGGTGGCGGGGGCGGAGGCGCCAAGCCTCTCGTCGCCA[C/T]
CCTCGGGCTTGGACGCAGCGGCGAGGTGGTCCGCGCGCTGCTCCAGACAAGCGAGCGCGACTTTGAGGTCGCCATGGACAGAGATGGGGCCACCGGGGCC
Reverse complement sequence
GGCCCCGGTGGCCCCATCTCTGTCCATGGCGACCTCAAAGTCGCGCTCGCTTGTCTGGAGCAGCGCGCGGACCACCTCGCCGCTGCGTCCAAGCCCGAGG[G/A]
TGGCGACGAGAGGCTTGGCGCCTCCGCCCCCGCCACCCCGAGGCAGCGGATGATCACAGGCGACGAGGTCCCGGTCAAGGAGGTTGCCCTGGGCGACGGC
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 | 7.50% | 0.70% | 2.69% | 89.19% | NA |
| All Indica | 2759 | 0.90% | 1.00% | 3.55% | 94.56% | NA |
| All Japonica | 1512 | 20.40% | 0.20% | 0.99% | 78.44% | NA |
| Aus | 269 | 2.20% | 0.00% | 2.23% | 95.54% | NA |
| Indica I | 595 | 0.50% | 1.70% | 1.85% | 95.97% | NA |
| Indica II | 465 | 0.90% | 0.90% | 1.29% | 96.99% | NA |
| Indica III | 913 | 0.80% | 0.70% | 5.91% | 92.66% | NA |
| Indica Intermediate | 786 | 1.30% | 1.00% | 3.44% | 94.27% | NA |
| Temperate Japonica | 767 | 38.30% | 0.10% | 0.78% | 60.76% | NA |
| Tropical Japonica | 504 | 1.00% | 0.40% | 1.19% | 97.42% | NA |
| Japonica Intermediate | 241 | 3.70% | 0.00% | 1.24% | 95.02% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 2.08% | 96.88% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 6.67% | 77.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001308 | C -> T | LOC_Os01g74230.1 | missense_variant ; p.Gly589Asp; MODERATE | nonsynonymous_codon ; G589D | Average:14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308 | benign  |
0.592 |
DELETERIOUS | 0.02 |
| vg0143001308 | C -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |