Search for Variation information by Variation ID:
Detailed information for vg0905621428:
| Variant ID: vg0905621428 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5621428 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATAATCTCTTCCTCCAGCTTCAAACATCATTGATGGAAGGTCTTCACGATCACTAGTCAACGTCATGCGAACACGACTATTCTCCTCATTGGGGTCATGG[G/T,A]
GAATTTGGCGATACTCGGGGACAATGTTGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTACTGCATCGATCAAGCTTTCTGGCAT
Reverse complement sequence
ATGCCAGAAAGCTTGATCGATGCAGTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACAACATTGTCCCCGAGTATCGCCAAATTC[C/A,T]
CCATGACCCCAATGAGGAGAATAGTCGTGTTCGCATGACGTTGACTAGTGATCGTGAAGACCTTCCATCAATGATGTTTGAAGCTGGAGGAAGAGATTAT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 2.30% | 0.00% | 0.00% | A: 0.02% |
| All Indica | 2759 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.00% | A: 0.07% |
| Aus | 269 | 87.40% | 12.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.00% | A: 0.20% |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905621428 | G -> T | LOC_Os09g10310.1 | missense_variant ; p.Pro34His; MODERATE | nonsynonymous_codon ; P34Q | Average:39.451; most accessible tissue: Callus, score: 57.912 | possibly damaging  |
1.986 |
DELETERIOUS | 0.00 |
| vg0905621428 | G -> A | LOC_Os09g10310.1 | missense_variant ; p.Pro34Leu; MODERATE | nonsynonymous_codon ; P34L | Average:39.451; most accessible tissue: Callus, score: 57.912 | benign |
1.461 |
DELETERIOUS | 0.00 |