Search for Variation information by Variation ID:
Detailed information for vg1007752734:
| Variant ID: vg1007752734 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7752734 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
TCATAGGTGCCTCGAAAGTTAAGGACAAAGACATCACGCAATTGCTTCCATGAGTAAATGCTATTGGCTGGTAAATTGAAATACCAAGAACGGACGATGC[C/T]
GTCTAGAGCGAGATGTATTACCTTTGCCTTGGTATTTTCGTCGCCATGAGCCGCTTCGATCGCGGACTCATAAATGGAGAGGAATTCTTTTGGGTCAGTT
Reverse complement sequence
AACTGACCCAAAAGAATTCCTCTCCATTTATGAGTCCGCGATCGAAGCGGCTCATGGCGACGAAAATACCAAGGCAAAGGTAATACATCTCGCTCTAGAC[G/A]
GCATCGTCCGTTCTTGGTATTTCAATTTACCAGCCAATAGCATTTACTCATGGAAGCAATTGCGTGATGTCTTTGTCCTTAACTTTCGAGGCACCTATGA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.30% | 4.00% | 4.63% | 0.00% | NA |
| All Indica | 2759 | 85.80% | 6.70% | 7.47% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.30% | 0.33% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 69.10% | 7.40% | 23.53% | 0.00% | NA |
| Indica II | 465 | 85.80% | 9.20% | 4.95% | 0.00% | NA |
| Indica III | 913 | 96.60% | 3.00% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 86.00% | 9.00% | 4.96% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 8.89% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1007752734 | C -> T | LOC_Os10g14795.1 | missense_variant ; p.Gly291Ser; MODERATE | nonsynonymous_codon ; G291S | Average:53.026; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 | benign  |
0.756 |
TOLERATED | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1007752734 | 3.44E-06 | NA | mr1495 | Ind_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 |