Search for Variation information by Variation ID:
Detailed information for vg0409515514:
| Variant ID: vg0409515514 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515514 |
| 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, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
ATCGGCCATAAGGTTATAATATTCATCGGCTATCAAACCGTCTTGCAATTCTATCCTTCTAGAGCCGATTCTAACTTCCCATGGCAAAACAGCTTCATGT[C/T]
CATAAACAAGCTTATAAGGAGGAACTTGAATATTGATCCATGACAAGCCATCCGATAAGACCACAATGCTTCGGCCAACCGGGTATGCCATTGCTGAGGA
Reverse complement sequence
TCCTCAGCAATGGCATACCCGGTTGGCCGAAGCATTGTGGTCTTATCGGATGGCTTGTCATGGATCAATATTCAAGTTCCTCCTTATAAGCTTGTTTATG[G/A]
ACATGAAGCTGTTTTGCCATGGGAAGTTAGAATCGGCTCTAGAAGGATAGAATTGCAAGACGGTTTGATAGCCGATGAATATTATAACCTTATGGCCGAT
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 | 90.30% | 0.00% | 0.72% | 8.93% | NA |
| All Indica | 2759 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 73.00% | 0.10% | 0.86% | 26.06% | NA |
| Aus | 269 | 100.00% | 0.00% | 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 | 99.30% | 0.00% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 30.80% | 0.00% | 2.18% | 67.06% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.40% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 58.30% | 1.00% | 12.50% | 28.12% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 3.33% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515514 | C -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:23.481; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |
| vg0409515514 | C -> T | LOC_Os04g17380.1 | missense_variant ; p.Gly31Glu; MODERATE | nonsynonymous_codon ; G31E | Average:23.481; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | probably damaging  |
2.581 |
DELETERIOUS | 0.02 |