Search for Variation information by Variation ID:
Detailed information for vg0136012464:
| Variant ID: vg0136012464 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36012464 |
| Reference Allele: T | Alternative Allele: C |
| 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: 327. )
Flanking Sequence (100 bp) in Reference Genome:
GTGGTGTCCTGGAACGCGTTGATCTGCGGATATGCGCAAAATGGGAGGGGGGAGGAGGCTTTGGATGCCTTCAGGAGGATGAAAGCTACAGGCTTGAAGC[T/C]
GGATCGTGTTACTCTTCTTGGCTTGCTGTTTGGTTGCAACCATGCTGGTCTGGTTGATGAAGGTTACTCATTGTTCAGGACTGCCGAGATGGAGCAGCCG
Reverse complement sequence
CGGCTGCTCCATCTCGGCAGTCCTGAACAATGAGTAACCTTCATCAACCAGACCAGCATGGTTGCAACCAAACAGCAAGCCAAGAAGAGTAACACGATCC[A/G]
GCTTCAAGCCTGTAGCTTTCATCCTCCTGAAGGCATCCAAAGCCTCCTCCCCCCTCCCATTTTGCGCATATCCGCAGATCAACGCGTTCCAGGACACCAC
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 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 2.00% | 98.00% | 0.00% | 0.00% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.80% | 97.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 53.30% | 46.70% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136012464 | T -> C | LOC_Os01g62220.1 | missense_variant ; p.Leu272Pro; MODERATE | nonsynonymous_codon ; L272P | Average:74.714; most accessible tissue: Callus, score: 86.839 | possibly damaging  |
-1.746 |
TOLERATED | 1.00 |