Search for Variation information by Variation ID:
Detailed information for vg0319758392:
| Variant ID: vg0319758392 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19758392 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGTAATCTTGGCGAGGATTTGTGTTGCCTTGATGCTTCTCTCCGTTGGAACTGGCGGGTTGGTTGGCCATTTTCTTCGTCAGCAAAAAACTGAATTGAC[A/G]
ATCTTTTGGTACATGATCAGTTCCTTCACAAAAGAAACAAGTGATCCTGCTCGTTGGACACCTGTCGGGTGGATGGTCTTCCTCACAATGAACGCATGTA
Reverse complement sequence
TACATGCGTTCATTGTGAGGAAGACCATCCACCCGACAGGTGTCCAACGAGCAGGATCACTTGTTTCTTTTGTGAAGGAACTGATCATGTACCAAAAGAT[T/C]
GTCAATTCAGTTTTTTGCTGACGAAGAAAATGGCCAACCAACCCGCCAGTTCCAACGGAGAGAAGCATCAAGGCAACACAAATCCTCGCCAAGATTACAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.40% | 1.40% | 17.29% | 50.85% | NA |
| All Indica | 2759 | 3.60% | 0.10% | 24.97% | 71.33% | NA |
| All Japonica | 1512 | 78.80% | 4.20% | 4.43% | 12.50% | NA |
| Aus | 269 | 11.50% | 0.00% | 12.27% | 76.21% | NA |
| Indica I | 595 | 2.70% | 0.00% | 16.30% | 81.01% | NA |
| Indica II | 465 | 4.50% | 0.00% | 22.15% | 73.33% | NA |
| Indica III | 913 | 2.50% | 0.20% | 32.97% | 64.29% | NA |
| Indica Intermediate | 786 | 5.10% | 0.00% | 23.92% | 70.99% | NA |
| Temperate Japonica | 767 | 94.10% | 0.30% | 1.56% | 4.04% | NA |
| Tropical Japonica | 504 | 61.10% | 4.40% | 8.73% | 25.79% | NA |
| Japonica Intermediate | 241 | 67.20% | 16.60% | 4.56% | 11.62% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 8.33% | 17.71% | NA |
| Intermediate | 90 | 50.00% | 1.10% | 22.22% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319758392 | A -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:5.314; most accessible tissue: Callus, score: 10.812 | N | N | N | N |
| vg0319758392 | A -> G | LOC_Os03g35670.1 | missense_variant ; p.Cys252Arg; MODERATE | nonsynonymous_codon ; C252R | Average:5.314; most accessible tissue: Callus, score: 10.812 | probably damaging  |
2.24 |
DELETERIOUS | 0.00 |