Search for Variation information by Variation ID:
Detailed information for vg0408160817:
| Variant ID: vg0408160817 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 8160817 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.53, C: 0.47, others allele: 0.00, population size: 96. )
Flanking Sequence (100 bp) in Reference Genome:
CCAGACGGTACCTTGATGCTCTCCAAGCATTCAAACATACTTTCCTTCTCTGCCTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGCTTCCTTTCT[T/C]
CTTTGGTTCCGGATGAAGGTCACCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCAACTTTCCATATACACCTAGGAAGCCA
Reverse complement sequence
TGGCTTCCTAGGTGTATATGGAAAGTTGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGTGACCTTCATCCGGAACCAAAG[A/G]
AGAAAGGAAGCCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAGGCAGAGAAGGAAAGTATGTTTGAATGCTTGGAGAGCATCAAGGTACCGTCTGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.50% | 3.40% | 36.39% | 25.77% | NA |
| All Indica | 2759 | 21.30% | 5.50% | 53.03% | 20.19% | NA |
| All Japonica | 1512 | 63.60% | 0.20% | 0.99% | 35.25% | NA |
| Aus | 269 | 14.90% | 0.00% | 69.89% | 15.24% | NA |
| Indica I | 595 | 29.40% | 0.00% | 47.90% | 22.69% | NA |
| Indica II | 465 | 26.90% | 21.70% | 34.62% | 16.77% | NA |
| Indica III | 913 | 15.40% | 3.00% | 61.99% | 19.61% | NA |
| Indica Intermediate | 786 | 18.60% | 3.10% | 57.38% | 20.99% | NA |
| Temperate Japonica | 767 | 96.10% | 0.10% | 0.39% | 3.39% | NA |
| Tropical Japonica | 504 | 11.10% | 0.20% | 1.59% | 87.10% | NA |
| Japonica Intermediate | 241 | 69.70% | 0.40% | 1.66% | 28.22% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 20.83% | 70.83% | NA |
| Intermediate | 90 | 36.70% | 4.40% | 37.78% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0408160817 | T -> C | LOC_Os04g14560.1 | missense_variant ; p.Lys686Glu; MODERATE | nonsynonymous_codon ; K686E | Average:7.782; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
-0.712 |
TOLERATED | 1.00 |
| vg0408160817 | T -> DEL | LOC_Os04g14560.1 | N | frameshift_variant | Average:7.782; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0408160817 | 1.56E-06 | 7.88E-07 | mr1167_2 | 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 |
| vg0408160817 | 1.70E-06 | 1.70E-06 | mr1574_2 | 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 |