Search for Variation information by Variation ID:
Detailed information for vg0407784068:
| Variant ID: vg0407784068 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 7784068 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.09, others allele: 0.00, population size: 159. )
Flanking Sequence (100 bp) in Reference Genome:
AAACAAGTACCCTCTTCCTCGGATCGATGATCTGTTCGACCAACTCAAAAGTGCCACCGTCTTTTCTAAAATCGACCTTCGCTCCGGATATCACCAATTG[C/T]
GTATTCGTGAAGAAGATATCCCGAAGACCGCATTCACCACGCGATATGGGCTGTATGAATTCACGGTGATGTCGTTCGGTCTGACTAATGCTCCTTCCTT
Reverse complement sequence
AAGGAAGGAGCATTAGTCAGACCGAACGACATCACCGTGAATTCATACAGCCCATATCGCGTGGTGAATGCGGTCTTCGGGATATCTTCTTCACGAATAC[G/A]
CAATTGGTGATATCCGGAGCGAAGGTCGATTTTAGAAAAGACGGTGGCACTTTTGAGTTGGTCGAACAGATCATCGATCCGAGGAAGAGGGTACTTGTTT
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 | 85.40% | 7.10% | 1.35% | 6.14% | NA |
| All Indica | 2759 | 91.50% | 7.70% | 0.72% | 0.04% | NA |
| All Japonica | 1512 | 72.20% | 7.70% | 1.52% | 18.52% | NA |
| Aus | 269 | 90.00% | 0.70% | 7.81% | 1.49% | NA |
| Indica I | 595 | 98.80% | 0.70% | 0.50% | 0.00% | NA |
| Indica II | 465 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 83.50% | 15.90% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 93.00% | 5.50% | 1.40% | 0.13% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.00% | 2.35% | NA |
| Tropical Japonica | 504 | 30.40% | 21.80% | 3.57% | 44.25% | NA |
| Japonica Intermediate | 241 | 78.80% | 2.90% | 2.07% | 16.18% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 5.60% | 0.00% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0407784068 | C -> DEL | LOC_Os04g13930.1 | N | frameshift_variant | Average:15.309; most accessible tissue: Callus, score: 23.171 | N | N | N | N |
| vg0407784068 | C -> T | LOC_Os04g13930.1 | missense_variant ; p.Arg860Cys; MODERATE | nonsynonymous_codon ; R860C | Average:15.309; most accessible tissue: Callus, score: 23.171 | probably damaging  |
2.729 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0407784068 | NA | 1.25E-06 | mr1238 | Ind_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 |
| vg0407784068 | NA | 1.62E-06 | mr1309 | Ind_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 |
| vg0407784068 | 6.97E-06 | 1.42E-07 | mr1835 | 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 |
| vg0407784068 | NA | 5.37E-08 | mr1841 | Ind_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 |
| vg0407784068 | 8.48E-06 | 8.48E-06 | mr1900 | Ind_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 |
| vg0407784068 | NA | 4.60E-06 | mr1964 | 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 |
| vg0407784068 | NA | 6.47E-07 | mr1121_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 |
| vg0407784068 | NA | 4.77E-06 | mr1239_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 |
| vg0407784068 | NA | 6.74E-07 | mr1841_2 | Ind_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 |