Search for Variation information by Variation ID:
Detailed information for vg0512045572:
| Variant ID: vg0512045572 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045572 |
| 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: 227. )
Flanking Sequence (100 bp) in Reference Genome:
CACAGTCTCCGCACGACTTTCATCCATAGCCCACAACATCTCAACCAAATGCTTCGTGGTAGCATCATTCTCAATTCCTTCAGTCTCAAGGTAACTGCCA[C/T]
GGTCACTTCCCTGGGGTTGGCGAGGATGGTAGCGATACTCAGTGTCGGCCAATTGATCACTGTAGCGATCACGGAGCTCTCCTATGGCGATCCTTGCCAC
Reverse complement sequence
GTGGCAAGGATCGCCATAGGAGAGCTCCGTGATCGCTACAGTGATCAATTGGCCGACACTGAGTATCGCTACCATCCTCGCCAACCCCAGGGAAGTGACC[G/A]
TGGCAGTTACCTTGAGACTGAAGGAATTGAGAATGATGCTACCACGAAGCATTTGGTTGAGATGTTGTGGGCTATGGATGAAAGTCGTGCGGAGACTGTG
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 | 84.30% | 0.30% | 3.11% | 12.29% | NA |
| All Indica | 2759 | 86.20% | 0.00% | 4.89% | 8.92% | NA |
| All Japonica | 1512 | 91.00% | 1.00% | 0.46% | 7.54% | NA |
| Aus | 269 | 21.60% | 0.00% | 0.74% | 77.70% | NA |
| Indica I | 595 | 92.10% | 0.00% | 3.19% | 4.71% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.86% | 1.51% | NA |
| Indica III | 913 | 76.30% | 0.00% | 9.53% | 14.13% | NA |
| Indica Intermediate | 786 | 86.30% | 0.10% | 3.18% | 10.43% | NA |
| Temperate Japonica | 767 | 85.80% | 0.00% | 0.65% | 13.56% | NA |
| Tropical Japonica | 504 | 96.00% | 3.00% | 0.20% | 0.79% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 1.11% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045572 | C -> T | LOC_Os05g20520.1 | missense_variant ; p.Arg137His; MODERATE | nonsynonymous_codon ; R137H | Average:8.384; most accessible tissue: Zhenshan97 flower, score: 19.041 | benign  |
0.442 |
DELETERIOUS | 0.03 |
| vg0512045572 | C -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:8.384; most accessible tissue: Zhenshan97 flower, score: 19.041 | N | N | N | N |