Search for Variation information by Variation ID:
Detailed information for vg0206203920:
| Variant ID: vg0206203920 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6203920 |
| 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: 327. )
Flanking Sequence (100 bp) in Reference Genome:
TAATCACCATGGAAATCTTTTGCACCACATCATATTATCACATCATACTTTCACCTATTTCCAGCGCATTCGATGGAAGAAGCTGAATTTCTATGCGATC[G/A]
GATAGGAATTATCGCAAACGGCAGCTTGCAATGCATCGGGAACTCTAAAGAGGTACATCTACACATGTAAACTGATCACATATTTCATATATGGCCATTG
Reverse complement sequence
CAATGGCCATATATGAAATATGTGATCAGTTTACATGTGTAGATGTACCTCTTTAGAGTTCCCGATGCATTGCAAGCTGCCGTTTGCGATAATTCCTATC[C/T]
GATCGCATAGAAATTCAGCTTCTTCCATCGAATGCGCTGGAAATAGGTGAAAGTATGATGTGATAATATGATGTGGTGCAAAAGATTTCCATGGTGATTA
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 | 98.30% | 1.40% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 94.70% | 4.30% | 0.99% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.20% | 0.90% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 94.00% | 5.00% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.10% | 13.70% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0206203920 | G -> A | LOC_Os02g11960.1 | missense_variant ; p.Arg847Gln; MODERATE | nonsynonymous_codon ; R847Q | Average:24.734; most accessible tissue: Zhenshan97 panicle, score: 39.652 | probably damaging  |
2.108 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206203920 | 4.20E-06 | 4.08E-09 | mr1750_2 | Jap_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 |