Search for Variation information by Variation ID:
Detailed information for vg0809844393:
| Variant ID: vg0809844393 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9844393 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 300. )
Flanking Sequence (100 bp) in Reference Genome:
TGAGGAGCATTTATCAAAGGTCCGACAGGACAATATTGGTCGATCATATATTTGGATCAACAGAGAACATGGTGCTTGCTTCAACGAATGGTTCAAGGAT[C/T]
GTGTAGCACGGTCGACCGATGGCCCAAGTGAGATATTACAAAGGTTGGCAAGGGGTCCATCTTGGGATGTTGACACATGGCAAGGGTACGATATCAATGG
Reverse complement sequence
CCATTGATATCGTACCCTTGCCATGTGTCAACATCCCAAGATGGACCCCTTGCCAACCTTTGTAATATCTCACTTGGGCCATCGGTCGACCGTGCTACAC[G/A]
ATCCTTGAACCATTCGTTGAAGCAAGCACCATGTTCTCTGTTGATCCAAATATATGATCGACCAATATTGTCCTGTCGGACCTTTGATAAATGCTCCTCA
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 | 84.20% | 10.80% | 3.47% | 1.54% | NA |
| All Indica | 2759 | 84.80% | 7.30% | 5.33% | 2.61% | NA |
| All Japonica | 1512 | 85.30% | 14.20% | 0.53% | 0.00% | NA |
| Aus | 269 | 98.50% | 0.40% | 1.12% | 0.00% | NA |
| Indica I | 595 | 95.60% | 2.00% | 1.51% | 0.84% | NA |
| Indica II | 465 | 91.60% | 6.50% | 1.08% | 0.86% | NA |
| Indica III | 913 | 73.90% | 9.00% | 11.50% | 5.59% | NA |
| Indica Intermediate | 786 | 85.10% | 9.80% | 3.56% | 1.53% | NA |
| Temperate Japonica | 767 | 92.80% | 7.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 70.60% | 28.20% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 91.70% | 7.50% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 85.40% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 13.30% | 3.33% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809844393 | C -> T | LOC_Os08g16140.1 | missense_variant ; p.Arg796Cys; MODERATE | nonsynonymous_codon ; R796C | Average:28.947; most accessible tissue: Minghui63 young leaf, score: 39.381 | probably damaging  |
3.16 |
TOLERATED | 0.07 |
| vg0809844393 | C -> DEL | LOC_Os08g16140.1 | N | frameshift_variant | Average:28.947; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809844393 | NA | 2.15E-08 | mr1136_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 |
| vg0809844393 | 9.17E-07 | 9.16E-07 | mr1541_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 |
| vg0809844393 | NA | 1.27E-06 | mr1798_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 |