Search for Variation information by Variation ID:
Detailed information for vg0905621452:
| Variant ID: vg0905621452 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5621452 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
CATCATTGATGGAAGGTCTTCACGATCACTAGTCAACGTCATGCGAACACGACTATTCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACA[A/T]
TGTTGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTACTGCATCGATCAAGCTTTCTGGCATCTAAAGGAACACATAAAGGAGGAA
Reverse complement sequence
TTCCTCCTTTATGTGTTCCTTTAGATGCCAGAAAGCTTGATCGATGCAGTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACAACA[T/A]
TGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGAATAGTCGTGTTCGCATGACGTTGACTAGTGATCGTGAAGACCTTCCATCAATGATG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 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 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 78.10% | 21.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905621452 | A -> T | LOC_Os09g10310.1 | missense_variant ; p.Ile26Asn; MODERATE | nonsynonymous_codon ; I26N | Average:39.002; most accessible tissue: Callus, score: 57.912 | possibly damaging  |
1.6 |
TOLERATED | 0.16 |