Search for Variation information by Variation ID:
Detailed information for vg0725421277:
| Variant ID: vg0725421277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421277 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, C: 0.27, others allele: 0.00, population size: 41. )
Flanking Sequence (100 bp) in Reference Genome:
GGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCGACTGGTGATGCCACGGATTTGTCGACCCTCT[G/C]
AAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTCGTCGCCGCTCACACTCGGA
Reverse complement sequence
TCCGAGTGTGAGCGGCGACGACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTT[C/G]
AGAGGGTCGACAAATCCGTGGCATCACCAGTCGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.50% | 2.80% | 1.90% | 74.76% | NA |
| All Indica | 2759 | 1.40% | 2.60% | 2.39% | 93.58% | NA |
| All Japonica | 1512 | 59.20% | 0.70% | 0.53% | 39.62% | NA |
| Aus | 269 | 0.40% | 1.50% | 1.12% | 97.03% | NA |
| Indica I | 595 | 2.20% | 1.80% | 3.03% | 92.94% | NA |
| Indica II | 465 | 1.50% | 1.30% | 1.29% | 95.91% | NA |
| Indica III | 913 | 0.20% | 4.50% | 1.97% | 93.32% | NA |
| Indica Intermediate | 786 | 2.30% | 1.70% | 3.05% | 93.00% | NA |
| Temperate Japonica | 767 | 89.20% | 0.10% | 0.00% | 10.69% | NA |
| Tropical Japonica | 504 | 12.70% | 0.60% | 0.99% | 85.71% | NA |
| Japonica Intermediate | 241 | 61.00% | 2.50% | 1.24% | 35.27% | NA |
| VI/Aromatic | 96 | 12.50% | 47.90% | 2.08% | 37.50% | NA |
| Intermediate | 90 | 25.60% | 1.10% | 12.22% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421277 | G -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421277 | G -> C | LOC_Os07g42460.1 | missense_variant ; p.Gln45Glu; MODERATE | nonsynonymous_codon ; Q45E | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | possibly damaging  |
-1.669 |
TOLERATED | 1.00 |