Search for Variation information by Variation ID:
Detailed information for vg0704594515:
| Variant ID: vg0704594515 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4594515 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 322. )
Flanking Sequence (100 bp) in Reference Genome:
GGAGCTATGGGGTGGAACATGTCTGTTGAACTTGTGTTGTTTTGTTTACCAGATGCACAATCTAAGGGAGTATCTCTGATGCACCCTCCAATCGGATCAC[C/T]
GGCATCCCAATCCTGCGGTGACTTGGGAGAGAAGCTCTCCATACATCCACAGAATGGGACTGAATTGCCATTGCAGACCGTGAAAGGTCCACAGACATCG
Reverse complement sequence
CGATGTCTGTGGACCTTTCACGGTCTGCAATGGCAATTCAGTCCCATTCTGTGGATGTATGGAGAGCTTCTCTCCCAAGTCACCGCAGGATTGGGATGCC[G/A]
GTGATCCGATTGGAGGGTGCATCAGAGATACTCCCTTAGATTGTGCATCTGGTAAACAAAACAACACAAGTTCAACAGACATGTTCCACCCCATAGCTCC
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 | 87.50% | 12.10% | 0.34% | 0.00% | NA |
| All Indica | 2759 | 94.80% | 5.10% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 71.90% | 27.30% | 0.79% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.10% | 12.60% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.00% | 4.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 50.50% | 48.00% | 1.56% | 0.00% | NA |
| Tropical Japonica | 504 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 87.60% | 12.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704594515 | C -> T | LOC_Os07g08860.1 | missense_variant ; p.Gly365Ser; MODERATE | nonsynonymous_codon ; G365S | Average:64.493; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | benign  |
1.164 |
TOLERATED | 0.17 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0704594515 | NA | 5.82E-07 | mr1707 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0704594515 | NA | 4.41E-07 | mr1860 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0704594515 | NA | 1.20E-07 | mr1707_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |