Search for Variation information by Variation ID:
Detailed information for vg1214649624:
| Variant ID: vg1214649624 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14649624 |
| Reference Allele: G | Alternative Allele: C,A |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, G: 0.44, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
GAGTAAGTTCACGGTTACCGTTATGTGGTCGACGGCGCTGTCGACCGATGTTGGATTTTCCACCAACTCAGTTGATGCGCAACTGCTGCGTTTTTGGGTG[G/C,A]
GACTTCCTAACTCTTTGTGCGCAGCAGCAGCGGCGGCCTGGGGGTTCTGTTGCTCTACTCGGATCTCTTGCCTAATCTTAGCCCTCATTGACTCGAGCTT
Reverse complement sequence
AAGCTCGAGTCAATGAGGGCTAAGATTAGGCAAGAGATCCGAGTAGAGCAACAGAACCCCCAGGCCGCCGCTGCTGCTGCGCACAAAGAGTTAGGAAGTC[C/G,T]
CACCCAAAAACGCAGCAGTTGCGCATCAACTGAGTTGGTGGAAAATCCAACATCGGTCGACAGCGCCGTCGACCACATAACGGTAACCGTGAACTTACTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.80% | 10.60% | 0.23% | 17.16% | A: 0.25% |
| All Indica | 2759 | 67.10% | 3.40% | 0.29% | 28.78% | A: 0.43% |
| All Japonica | 1512 | 77.80% | 21.70% | 0.20% | 0.26% | NA |
| Aus | 269 | 81.00% | 18.60% | 0.00% | 0.37% | NA |
| Indica I | 595 | 80.20% | 0.00% | 0.00% | 19.50% | A: 0.34% |
| Indica II | 465 | 58.70% | 11.00% | 0.00% | 30.32% | NA |
| Indica III | 913 | 58.10% | 2.60% | 0.44% | 38.01% | A: 0.88% |
| Indica Intermediate | 786 | 72.60% | 2.40% | 0.51% | 24.17% | A: 0.25% |
| Temperate Japonica | 767 | 96.10% | 3.30% | 0.26% | 0.39% | NA |
| Tropical Japonica | 504 | 49.00% | 50.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 80.10% | 19.50% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 70.80% | 19.80% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 87.80% | 8.90% | 0.00% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214649624 | G -> C | LOC_Os12g25390.1 | missense_variant ; p.Pro345Arg; MODERATE | nonsynonymous_codon ; P345R | Average:19.871; most accessible tissue: Minghui63 panicle, score: 46.754 | probably damaging  |
2.379 |
DELETERIOUS | 0.00 |
| vg1214649624 | G -> DEL | LOC_Os12g25390.1 | N | frameshift_variant | Average:19.871; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg1214649624 | G -> A | LOC_Os12g25390.1 | missense_variant ; p.Pro345Leu; MODERATE | nonsynonymous_codon ; P345L | Average:19.871; most accessible tissue: Minghui63 panicle, score: 46.754 | probably damaging |
2.029 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214649624 | 6.77E-07 | 6.77E-07 | mr1499 | 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 |
| vg1214649624 | NA | 8.09E-06 | mr1634 | 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 |
| vg1214649624 | 8.25E-07 | 1.64E-08 | mr1727 | 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 |
| vg1214649624 | NA | 4.61E-07 | mr1756 | 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 |
| vg1214649624 | 1.25E-06 | 1.25E-06 | mr1840 | 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 |