Search for Variation information by Variation ID:
Detailed information for vg1204379459:
| Variant ID: vg1204379459 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4379459 |
| 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, others allele: 0.00, population size: 49. )
Flanking Sequence (100 bp) in Reference Genome:
CTCTGGAGGCTACGCCGATTTTGAGAAGCTGGTTGACAAAGCAATCCATCAGGAGGATCAGTGCAACAAAATGGACAGGAAGAGAAAGGCAGCGCAATTC[C/T]
GGTCCAACCAAGGAAGCCACCCGCGACCGCGCTTCACTCCCAGACAGCAAAGTGGACCTACCACCATGATCGTCCGCCAGCACCGCCCTTTCAACTCGAG
Reverse complement sequence
CTCGAGTTGAAAGGGCGGTGCTGGCGGACGATCATGGTGGTAGGTCCACTTTGCTGTCTGGGAGTGAAGCGCGGTCGCGGGTGGCTTCCTTGGTTGGACC[G/A]
GAATTGCGCTGCCTTTCTCTTCCTGTCCATTTTGTTGCACTGATCCTCCTGATGGATTGCTTTGTCAACCAGCTTCTCAAAATCGGCGTAGCCTCCAGAG
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 | 37.20% | 16.40% | 12.63% | 33.79% | NA |
| All Indica | 2759 | 28.80% | 13.10% | 17.62% | 40.49% | NA |
| All Japonica | 1512 | 55.60% | 17.40% | 4.63% | 22.35% | NA |
| Aus | 269 | 25.70% | 48.00% | 10.78% | 15.61% | NA |
| Indica I | 595 | 34.80% | 21.70% | 23.36% | 20.17% | NA |
| Indica II | 465 | 29.70% | 6.00% | 9.03% | 55.27% | NA |
| Indica III | 913 | 22.10% | 9.60% | 19.06% | 49.18% | NA |
| Indica Intermediate | 786 | 31.40% | 14.90% | 16.67% | 37.02% | NA |
| Temperate Japonica | 767 | 80.80% | 0.50% | 6.13% | 12.52% | NA |
| Tropical Japonica | 504 | 27.60% | 45.60% | 1.59% | 25.20% | NA |
| Japonica Intermediate | 241 | 34.00% | 12.00% | 6.22% | 47.72% | NA |
| VI/Aromatic | 96 | 15.60% | 7.30% | 3.12% | 73.96% | NA |
| Intermediate | 90 | 43.30% | 14.40% | 10.00% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204379459 | C -> DEL | LOC_Os12g08620.1 | N | frameshift_variant | Average:11.692; most accessible tissue: Callus, score: 40.754 | N | N | N | N |
| vg1204379459 | C -> T | LOC_Os12g08620.1 | missense_variant ; p.Arg164Trp; MODERATE | nonsynonymous_codon ; R164W | Average:11.692; most accessible tissue: Callus, score: 40.754 | benign  |
0.417 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204379459 | NA | 3.65E-07 | mr1414 | 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 |
| vg1204379459 | 9.70E-06 | 9.70E-06 | mr1460 | 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 |
| vg1204379459 | 2.66E-06 | 2.66E-06 | mr1529 | 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 |
| vg1204379459 | NA | 6.55E-06 | mr1653 | 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 |
| vg1204379459 | NA | 5.24E-07 | mr1696 | 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 |