Search for Variation information by Variation ID:
Detailed information for vg0815412247:
| Variant ID: vg0815412247 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15412247 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 117. )
Flanking Sequence (100 bp) in Reference Genome:
TGCTGCTGCAGCTGTGCTTGCTGCTGCACCTGCTGCAACACCTGATGGTACTGTTGCTGCATCTGTTGCATCATCATTGTCATCATCTGAGTCTGATTGT[C/T]
CAACACCTGAGCAATTGTTGGGTTCTCGGGCGGTGGGGACGGACTGTTGTCAGATGCACCGTTGGCACGTGCTCCATTGGTCGGCTCTTCGCTGCCACTG
Reverse complement sequence
CAGTGGCAGCGAAGAGCCGACCAATGGAGCACGTGCCAACGGTGCATCTGACAACAGTCCGTCCCCACCGCCCGAGAACCCAACAATTGCTCAGGTGTTG[G/A]
ACAATCAGACTCAGATGATGACAATGATGATGCAACAGATGCAGCAACAGTACCATCAGGTGTTGCAGCAGGTGCAGCAGCAAGCACAGCTGCAGCAGCA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.10% | 6.60% | 7.28% | 66.10% | NA |
| All Indica | 2759 | 1.60% | 3.80% | 10.58% | 84.02% | NA |
| All Japonica | 1512 | 58.30% | 0.30% | 1.65% | 39.81% | NA |
| Aus | 269 | 0.00% | 72.90% | 5.58% | 21.56% | NA |
| Indica I | 595 | 0.20% | 0.20% | 1.85% | 97.82% | NA |
| Indica II | 465 | 2.60% | 1.30% | 7.53% | 88.60% | NA |
| Indica III | 913 | 1.60% | 3.70% | 18.73% | 75.90% | NA |
| Indica Intermediate | 786 | 2.20% | 8.00% | 9.54% | 80.28% | NA |
| Temperate Japonica | 767 | 83.70% | 0.00% | 0.39% | 15.91% | NA |
| Tropical Japonica | 504 | 27.40% | 0.60% | 1.79% | 70.24% | NA |
| Japonica Intermediate | 241 | 41.90% | 0.40% | 5.39% | 52.28% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 4.17% | 94.79% | NA |
| Intermediate | 90 | 23.30% | 6.70% | 8.89% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815412247 | C -> T | LOC_Os08g25330.1 | missense_variant ; p.Asp47Asn; MODERATE | nonsynonymous_codon ; D47N | Average:10.667; most accessible tissue: Zhenshan97 root, score: 20.427 | benign  |
1.329 |
DELETERIOUS | 0.04 |
| vg0815412247 | C -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:10.667; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |