Search for Variation information by Variation ID:
Detailed information for vg0611474586:
| Variant ID: vg0611474586 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11474586 |
| 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: 304. )
Flanking Sequence (100 bp) in Reference Genome:
AGACGGTGGAAGAGAGGGTTGACAACGCTCCCTACGCCTCTCTCCTTCCCCTTTTCGGCATATGGGTAGAAGAGGACGAAGCCATAGCCCTTAGATCTAC[C/T]
AGATTGCTTGTTGGAGATGACACAGCAGTCCTCGAGCTCACCGAAGAGGGAGAACGCAAAGTGGAGGTCGTCGGCTTCGGCGCCCCAGCCGAGGCCGTGG
Reverse complement sequence
CCACGGCCTCGGCTGGGGCGCCGAAGCCGACGACCTCCACTTTGCGTTCTCCCTCTTCGGTGAGCTCGAGGACTGCTGTGTCATCTCCAACAAGCAATCT[G/A]
GTAGATCTAAGGGCTATGGCTTCGTCCTCTTCTACCCATATGCCGAAAAGGGGAAGGAGAGAGGCGTAGGGAGCGTTGTCAACCCTCTCTTCCACCGTCT
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 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 38.50% | 61.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0611474586 | C -> T | LOC_Os06g20010.1 | missense_variant ; p.Gly53Ser; MODERATE | nonsynonymous_codon ; G53S | Average:73.403; most accessible tissue: Zhenshan97 young leaf, score: 90.175 | possibly damaging  |
1.927 |
DELETERIOUS | 0.01 |