Search for Variation information by Variation ID:
Detailed information for vg0630442915:
| Variant ID: vg0630442915 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 30442915 |
| 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: 318. )
Flanking Sequence (100 bp) in Reference Genome:
GACAATAAGAAAACCTCAAACGGAGAAACATAAATTATATGCACAACGACAAGAAGGGGCCAGAAAGGATGTCGAGTGTGCATTTGGCGTGTTGCAATCC[C/T]
GTTTTGATATTGTCAACCGTCCAGCACGGTTGTGGAAAAGGAATGATGTTGTTAATATAATGCAAGCTTGCGTTATCCTCCATAATATGATAGTGGAAGA
Reverse complement sequence
TCTTCCACTATCATATTATGGAGGATAACGCAAGCTTGCATTATATTAACAACATCATTCCTTTTCCACAACCGTGCTGGACGGTTGACAATATCAAAAC[G/A]
GGATTGCAACACGCCAAATGCACACTCGACATCCTTTCTGGCCCCTTCTTGTCGTTGTGCATATAATTTATGTTTCTCCGTTTGAGGTTTTCTTATTGTC
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 | 46.20% | 0.70% | 5.84% | 47.21% | NA |
| All Indica | 2759 | 31.80% | 1.10% | 7.03% | 60.06% | NA |
| All Japonica | 1512 | 64.70% | 0.30% | 4.83% | 30.16% | NA |
| Aus | 269 | 94.10% | 0.00% | 0.74% | 5.20% | NA |
| Indica I | 595 | 48.20% | 0.50% | 5.04% | 46.22% | NA |
| Indica II | 465 | 11.80% | 1.10% | 10.11% | 76.99% | NA |
| Indica III | 913 | 30.00% | 1.20% | 6.46% | 62.32% | NA |
| Indica Intermediate | 786 | 33.30% | 1.40% | 7.38% | 57.89% | NA |
| Temperate Japonica | 767 | 94.10% | 0.00% | 0.13% | 5.74% | NA |
| Tropical Japonica | 504 | 21.80% | 0.60% | 13.29% | 64.29% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.40% | 2.07% | 36.51% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 3.12% | 59.38% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 4.44% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0630442915 | C -> T | LOC_Os06g50290.1 | missense_variant ; p.Arg797Cys; MODERATE | nonsynonymous_codon ; R797C | Average:9.574; most accessible tissue: Callus, score: 19.121 | benign  |
0.686 |
TOLERATED | 0.06 |
| vg0630442915 | C -> DEL | LOC_Os06g50290.1 | N | frameshift_variant | Average:9.574; most accessible tissue: Callus, score: 19.121 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0630442915 | NA | 5.85E-06 | mr1064_2 | Jap_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 |
| vg0630442915 | 4.72E-06 | 7.06E-07 | mr1312_2 | 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 |
| vg0630442915 | NA | 9.86E-08 | mr1510_2 | 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 |
| vg0630442915 | 3.73E-07 | 2.34E-08 | mr1663_2 | 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 |
| vg0630442915 | 3.17E-06 | NA | mr1665_2 | 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 |