Search for Variation information by Variation ID:
Detailed information for vg0905621453:
| Variant ID: vg0905621453 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5621453 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 227. )
Flanking Sequence (100 bp) in Reference Genome:
ATCATTGATGGAAGGTCTTCACGATCACTAGTCAACGTCATGCGAACACGACTATTCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAA[T/C]
GTTGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTACTGCATCGATCAAGCTTTCTGGCATCTAAAGGAACACATAAAGGAGGAAT
Reverse complement sequence
ATTCCTCCTTTATGTGTTCCTTTAGATGCCAGAAAGCTTGATCGATGCAGTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACAAC[A/G]
TTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGAATAGTCGTGTTCGCATGACGTTGACTAGTGATCGTGAAGACCTTCCATCAATGAT
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 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 94.60% | 5.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 56.90% | 43.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.60% | 6.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.90% | 8.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905621453 | T -> C | LOC_Os09g10310.1 | missense_variant ; p.Ile26Val; MODERATE | nonsynonymous_codon ; I26V | Average:39.002; most accessible tissue: Callus, score: 57.912 | benign  |
-0.369 |
TOLERATED | 1.00 |