Search for Variation information by Variation ID:
Detailed information for vg0435226147:
| Variant ID: vg0435226147 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35226147 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATCTTCTGAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAACCTCTCTCCGAGTGTTAGC[G/A]
GTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGTGCTCGAGAGGGTCGAAGG
Reverse complement sequence
CCTTCGACCCTCTCGAGCACCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCAC[C/T]
GCTAACACTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTCAGAAGAT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.90% | 0.30% | 10.01% | 19.74% | NA |
| All Indica | 2759 | 50.90% | 0.00% | 16.64% | 32.48% | NA |
| All Japonica | 1512 | 98.30% | 0.90% | 0.53% | 0.20% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.37% | 7.43% | NA |
| Indica I | 595 | 31.60% | 0.00% | 24.87% | 43.53% | NA |
| Indica II | 465 | 40.60% | 0.00% | 21.94% | 37.42% | NA |
| Indica III | 913 | 64.70% | 0.00% | 9.53% | 25.74% | NA |
| Indica Intermediate | 786 | 55.50% | 0.00% | 15.52% | 29.01% | NA |
| Temperate Japonica | 767 | 98.20% | 1.30% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 0.20% | 0.60% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.20% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 85.60% | 1.10% | 3.33% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435226147 | G -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0435226147 | G -> A | LOC_Os04g59220.1 | missense_variant ; p.Gly16Ser; MODERATE | nonsynonymous_codon ; G16S | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | possibly damaging  |
1.834 |
DELETERIOUS | 0.00 |