Search for Variation information by Variation ID:
Detailed information for vg0234180503:
| Variant ID: vg0234180503 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34180503 |
| 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: 336. )
Flanking Sequence (100 bp) in Reference Genome:
TTCAACGTACTCGGGTGGTGGAATGATCATAAGATGTCATATCCTGTGCTATCAAAACTAGCACAGGATGTGTTGACGGTGCCCGTATCTTCGGTATCCT[C/T]
CGAATCAGCCTTCAGTCTATGCGGAAGAATTATCGAGGATAGGAGAACAAGTCTGAGCAGCGATCATGTGGAAATACTATTAAGCGTCAAAGACTGGGAA
Reverse complement sequence
TTCCCAGTCTTTGACGCTTAATAGTATTTCCACATGATCGCTGCTCAGACTTGTTCTCCTATCCTCGATAATTCTTCCGCATAGACTGAAGGCTGATTCG[G/A]
AGGATACCGAAGATACGGGCACCGTCAACACATCCTGTGCTAGTTTTGATAGCACAGGATATGACATCTTATGATCATTCCACCACCCGAGTACGTTGAA
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 | 51.90% | 0.30% | 4.91% | 42.81% | NA |
| All Indica | 2759 | 28.10% | 0.30% | 5.40% | 66.22% | NA |
| All Japonica | 1512 | 97.70% | 0.10% | 0.46% | 1.79% | NA |
| Aus | 269 | 42.00% | 0.00% | 23.05% | 34.94% | NA |
| Indica I | 595 | 21.20% | 0.00% | 1.85% | 76.97% | NA |
| Indica II | 465 | 18.30% | 0.20% | 2.58% | 78.92% | NA |
| Indica III | 913 | 35.40% | 0.50% | 8.00% | 56.08% | NA |
| Indica Intermediate | 786 | 30.80% | 0.10% | 6.74% | 62.34% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.39% | 2.09% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.40% | 1.24% | 4.15% | NA |
| VI/Aromatic | 96 | 27.10% | 8.30% | 12.50% | 52.08% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 2.22% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234180503 | C -> T | LOC_Os02g55830.1 | missense_variant ; p.Ser495Phe; MODERATE | nonsynonymous_codon ; S495F | Average:8.338; most accessible tissue: Callus, score: 24.171 | possibly damaging  |
1.806 |
DELETERIOUS | 0.00 |
| vg0234180503 | C -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:8.338; most accessible tissue: Callus, score: 24.171 | N | N | N | N |