Search for Variation information by Variation ID:
Detailed information for vg0402781867:
| Variant ID: vg0402781867 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2781867 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, G: 0.25, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
ATACATCGTGATTACCACAGAATAATTGAATAATTGTGAAATCGAAATAAACCTTGGATTCACCATTGAGATTCAATATTAGATAGTAGATTACCATACA[G/C]
ATGGCCAGGAATGCTAAAACAGCCTAGAAGGGCCAACAACAGAAGCAGAAGTCCTCGGCTACAGTTCGGCATCTGCTTGCCCATTTGTGTGATTGCTTTG
Reverse complement sequence
CAAAGCAATCACACAAATGGGCAAGCAGATGCCGAACTGTAGCCGAGGACTTCTGCTTCTGTTGTTGGCCCTTCTAGGCTGTTTTAGCATTCCTGGCCAT[C/G]
TGTATGGTAATCTACTATCTAATATTGAATCTCAATGGTGAATCCAAGGTTTATTTCGATTTCACAATTATTCAATTATTCTGTGGTAATCACGATGTAT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.50% | 17.50% | 0.91% | 13.12% | NA |
| All Indica | 2759 | 83.10% | 2.30% | 0.22% | 14.39% | NA |
| All Japonica | 1512 | 46.50% | 47.40% | 0.86% | 5.22% | NA |
| Aus | 269 | 61.00% | 1.10% | 1.86% | 36.06% | NA |
| Indica I | 595 | 95.80% | 2.50% | 0.17% | 1.51% | NA |
| Indica II | 465 | 73.50% | 4.30% | 0.43% | 21.72% | NA |
| Indica III | 913 | 82.00% | 0.10% | 0.11% | 17.74% | NA |
| Indica Intermediate | 786 | 80.30% | 3.60% | 0.25% | 15.90% | NA |
| Temperate Japonica | 767 | 20.60% | 78.50% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 78.20% | 6.50% | 0.60% | 14.68% | NA |
| Japonica Intermediate | 241 | 62.70% | 34.00% | 1.24% | 2.07% | NA |
| VI/Aromatic | 96 | 16.70% | 29.20% | 15.62% | 38.54% | NA |
| Intermediate | 90 | 68.90% | 15.60% | 4.44% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402781867 | G -> C | LOC_Os04g05500.1 | missense_variant ; p.Leu29Val; MODERATE | nonsynonymous_codon ; L29V | Average:19.21; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | benign  |
-0.9 |
TOLERATED | 1.00 |
| vg0402781867 | G -> DEL | LOC_Os04g05500.1 | N | frameshift_variant | Average:19.21; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402781867 | NA | 1.77E-07 | mr1252 | 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 |
| vg0402781867 | 1.82E-06 | NA | mr1864 | 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 |
| vg0402781867 | NA | 6.32E-11 | mr1864 | 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 |
| vg0402781867 | NA | 3.70E-07 | mr1521_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 |
| vg0402781867 | NA | 1.52E-06 | mr1763_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 |