Search for Variation information by Variation ID:
Detailed information for vg0611474634:
| Variant ID: vg0611474634 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11474634 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )
Flanking Sequence (100 bp) in Reference Genome:
CCCTTTTCGGCATATGGGTAGAAGAGGACGAAGCCATAGCCCTTAGATCTACCAGATTGCTTGTTGGAGATGACACAGCAGTCCTCGAGCTCACCGAAGA[G/A]
GGAGAACGCAAAGTGGAGGTCGTCGGCTTCGGCGCCCCAGCCGAGGCCGTGGACGAAGAGCTTCATGCTCGTGAGGTCGGCCTCCGTTGCACATAGCACA
Reverse complement sequence
TGTGCTATGTGCAACGGAGGCCGACCTCACGAGCATGAAGCTCTTCGTCCACGGCCTCGGCTGGGGCGCCGAAGCCGACGACCTCCACTTTGCGTTCTCC[C/T]
TCTTCGGTGAGCTCGAGGACTGCTGTGTCATCTCCAACAAGCAATCTGGTAGATCTAAGGGCTATGGCTTCGTCCTCTTCTACCCATATGCCGAAAAGGG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 94.60% | 5.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 9.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 88.50% | 11.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0611474634 | G -> A | LOC_Os06g20010.1 | missense_variant ; p.Leu37Phe; MODERATE | nonsynonymous_codon ; L37F | Average:74.079; most accessible tissue: Zhenshan97 young leaf, score: 90.638 | possibly damaging  |
1.668 |
DELETERIOUS | 0.02 |