Search for Variation information by Variation ID:
Detailed information for vg0710157771:
| Variant ID: vg0710157771 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10157771 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 250. )
Flanking Sequence (100 bp) in Reference Genome:
TCTTTTTGTCACACATATTTATCCATATCCTCAGATGAAAACCCTCTAAAATTTTTTGATCATTATAAATTTCATGGAGTAGCTCAGTCTTCCCTGTGCC[T/G]
CTTTCACCAAATATACAGATAGATGTGAGACTCTGCTCACTAGTAATGTCACCCTCATCAGAACCATCTGACAGTAAGCTGTTAATTATTCTTTGCTGGT
Reverse complement sequence
ACCAGCAAAGAATAATTAACAGCTTACTGTCAGATGGTTCTGATGAGGGTGACATTACTAGTGAGCAGAGTCTCACATCTATCTGTATATTTGGTGAAAG[A/C]
GGCACAGGGAAGACTGAGCTACTCCATGAAATTTATAATGATCAAAAAATTTTAGAGGGTTTTCATCTGAGGATATGGATAAATATGTGTGACAAAAAGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.90% | 7.50% | 1.65% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.40% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 74.40% | 21.80% | 3.84% | 0.00% | NA |
| Aus | 269 | 96.70% | 1.90% | 1.49% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.70% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 0.50% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 62.20% | 31.40% | 6.39% | 0.00% | NA |
| Tropical Japonica | 504 | 89.70% | 9.10% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 81.30% | 17.40% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 8.90% | 7.78% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0710157771 | T -> G | LOC_Os07g17230.1 | missense_variant ; p.Arg585Ser; MODERATE | nonsynonymous_codon ; R585S | Average:68.018; most accessible tissue: Callus, score: 84.203 | possibly damaging  |
-1.871 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0710157771 | 1.62E-06 | 1.62E-06 | mr1955 | 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 |