Search for Variation information by Variation ID:
Detailed information for vg0211856727:
| Variant ID: vg0211856727 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 11856727 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
GTAACATCCAGACCTGTGATCATAATGATATCTATGAGAGTTGGAGTCATCAGCCCTTGATTGAACAGAAAGGCATTGGTAGTGTTTGACCAGAAGTAAG[A/G]
AGCAGCTGCCATCAGGGGTTCATCTTTGGCCGAGTTCGCTATAGTAAGGTCAAGTGCTTGGCCGATTCCAATTTCATCCCAGTGAACCCTCTTGCTGGCT
Reverse complement sequence
AGCCAGCAAGAGGGTTCACTGGGATGAAATTGGAATCGGCCAAGCACTTGACCTTACTATAGCGAACTCGGCCAAAGATGAACCCCTGATGGCAGCTGCT[T/C]
CTTACTTCTGGTCAAACACTACCAATGCCTTTCTGTTCAATCAAGGGCTGATGACTCCAACTCTCATAGATATCATTATGATCACAGGTCTGGATGTTAC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.20% | 1.60% | 0.97% | 1.16% | NA |
| All Indica | 2759 | 99.50% | 0.00% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 89.60% | 4.90% | 1.92% | 3.57% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 98.70% | 0.00% | 1.29% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.10% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 72.60% | 12.90% | 4.37% | 10.12% | NA |
| Japonica Intermediate | 241 | 93.80% | 3.30% | 1.66% | 1.24% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 2.20% | 4.44% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0211856727 | A -> G | LOC_Os02g20120.1 | missense_variant ; p.Ser98Pro; MODERATE | nonsynonymous_codon ; S98P | Average:17.143; most accessible tissue: Zhenshan97 panicle, score: 28.447 | benign  |
0.37 |
DELETERIOUS | 0.01 |
| vg0211856727 | A -> DEL | LOC_Os02g20120.1 | N | frameshift_variant | Average:17.143; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0211856727 | 4.02E-08 | 4.02E-08 | mr1848 | 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 |