Search for Variation information by Variation ID:
Detailed information for vg0327370626:
| Variant ID: vg0327370626 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27370626 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 119. )
Flanking Sequence (100 bp) in Reference Genome:
GGCATGGTGGACTCCGCCATGGACCCGAGGAGCTCCATCTTGAACACCGGCGAGCGCGCGGCGAGCACGGCGCGGTGTGCATGAAACGTCTCGCTGCCGA[C/T]
GGAGAACAACACGTCCGAGCCGTCGGCACGGTCCGCGATGTCGTCGAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAGTGCCGTCGTCATCACCG
Reverse complement sequence
CGGTGATGACGACGGCACTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTCGACGACATCGCGGACCGTGCCGACGGCTCGGACGTGTTGTTCTCC[G/A]
TCGGCAGCGAGACGTTTCATGCACACCGCGCCGTGCTCGCCGCGCGCTCGCCGGTGTTCAAGATGGAGCTCCTCGGGTCCATGGCGGAGTCCACCATGCC
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 | 91.60% | 8.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.90% | 4.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.00% | 4.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 13.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327370626 | C -> T | LOC_Os03g48120.1 | missense_variant ; p.Val56Ile; MODERATE | nonsynonymous_codon ; V56I | Average:79.967; most accessible tissue: Zhenshan97 panicle, score: 90.268 | benign  |
0.877 |
TOLERATED | 0.13 |