Search for Variation information by Variation ID:
Detailed information for vg0522884888:
| Variant ID: vg0522884888 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 22884888 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
CATCGGGCCGCTCGCGGACCATCAGGTGGCGGCGTCTCTGAAAGAGAAGGTCGCCAAGGAGGCGTCTGATGCTGCTGCTGCTACTACAAGTGGTGGCAAT[G/A]
TTCCGACAAAGGGGAGGAAGTTCTCCTCTGTGAGCGGACATCATCGCAAGGCATCAACCCCCTCGGTAAGCTATCCTGTCGTCAGATCGTACAGCCAGAA
Reverse complement sequence
TTCTGGCTGTACGATCTGACGACAGGATAGCTTACCGAGGGGGTTGATGCCTTGCGATGATGTCCGCTCACAGAGGAGAACTTCCTCCCCTTTGTCGGAA[C/T]
ATTGCCACCACTTGTAGTAGCAGCAGCAGCATCAGACGCCTCCTTGGCGACCTTCTCTTTCAGAGACGCCGCCACCTGATGGTCCGCGAGCGGCCCGATG
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 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 65.10% | 34.90% | 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 | 100.00% | 0.00% | 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 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 75.00% | 25.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0522884888 | G -> A | LOC_Os05g39010.1 | missense_variant ; p.Val116Ile; MODERATE | nonsynonymous_codon ; V116I | Average:51.552; most accessible tissue: Zhenshan97 panicle, score: 65.386 | benign  |
0.533 |
TOLERATED | 0.13 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0522884888 | 1.97E-06 | 1.97E-06 | mr1396 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |