Search for Variation information by Variation ID:
Detailed information for vg0435227339:
| Variant ID: vg0435227339 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35227339 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.29, others allele: 0.00, population size: 27. )
Flanking Sequence (100 bp) in Reference Genome:
ACTACCGCGGAGCTTTTTCAGCTCGCGGACCGAGTGGCTCGCAAGGAGGAGGCCTGGACTTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCGCCC[T/C]
CGGGTCCGCCGCTCGGTCAGGGCGGCGGGACAGGAGGAGGAAGAAGAGGTCGGCCCATTCCGACGACGAGGGTCATGTCCTCGCCTTCGAAGGCGTTTCG
Reverse complement sequence
CGAAACGCCTTCGAAGGCGAGGACATGACCCTCGTCGTCGGAATGGGCCGACCTCTTCTTCCTCCTCCTGTCCCGCCGCCCTGACCGAGCGGCGGACCCG[A/G]
GGGCGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAAGTCCAGGCCTCCTCCTTGCGAGCCACTCGGTCCGCGAGCTGAAAAAGCTCCGCGGTAGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 12.10% | 1.12% | 53.26% | NA |
| All Indica | 2759 | 7.30% | 2.90% | 1.52% | 88.29% | NA |
| All Japonica | 1512 | 81.90% | 15.60% | 0.40% | 2.05% | NA |
| Aus | 269 | 5.20% | 85.50% | 0.37% | 8.92% | NA |
| Indica I | 595 | 5.70% | 1.00% | 2.02% | 91.26% | NA |
| Indica II | 465 | 4.70% | 0.20% | 1.08% | 93.98% | NA |
| Indica III | 913 | 5.80% | 2.80% | 1.64% | 89.70% | NA |
| Indica Intermediate | 786 | 11.70% | 6.00% | 1.27% | 81.04% | NA |
| Temperate Japonica | 767 | 98.80% | 0.40% | 0.65% | 0.13% | NA |
| Tropical Japonica | 504 | 50.80% | 45.20% | 0.20% | 3.77% | NA |
| Japonica Intermediate | 241 | 93.40% | 2.10% | 0.00% | 4.56% | NA |
| VI/Aromatic | 96 | 77.10% | 11.50% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 61.10% | 17.80% | 3.33% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435227339 | T -> C | LOC_Os04g59220.1 | missense_variant ; p.Leu413Pro; MODERATE | nonsynonymous_codon ; L413P | Average:6.408; most accessible tissue: Callus, score: 14.467 | probably damaging  |
-2.029 |
TOLERATED | 1.00 |
| vg0435227339 | T -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:6.408; most accessible tissue: Callus, score: 14.467 | N | N | N | N |