Search for Variation information by Variation ID:
Detailed information for vg0805870856:
| Variant ID: vg0805870856 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5870856 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )
Flanking Sequence (100 bp) in Reference Genome:
ACATTGAGACTGGTCCCAAAGATCAATATGTCATCGACATATAAGCACAAGATCAATCCTTCTCCCCCACCATAGCGATAGTACACACATTTGTCAGTTT[C/T]
GTTCACAACAAAGCCAGCAGATGTAAGTGTGGTCTCAAACTTCTCATGCCATTGCTTAGGTGCTTGCTTAAGGCCATACAAGGATTTCAACAGTTTACAC
Reverse complement sequence
GTGTAAACTGTTGAAATCCTTGTATGGCCTTAAGCAAGCACCTAAGCAATGGCATGAGAAGTTTGAGACCACACTTACATCTGCTGGCTTTGTTGTGAAC[G/A]
AAACTGACAAATGTGTGTACTATCGCTATGGTGGGGGAGAAGGATTGATCTTGTGCTTATATGTCGATGACATATTGATCTTTGGGACCAGTCTCAATGT
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 | 39.70% | 4.00% | 5.88% | 50.40% | NA |
| All Indica | 2759 | 10.30% | 6.60% | 9.06% | 74.05% | NA |
| All Japonica | 1512 | 95.60% | 0.10% | 0.20% | 4.03% | NA |
| Aus | 269 | 15.60% | 0.00% | 6.69% | 77.70% | NA |
| Indica I | 595 | 14.50% | 0.00% | 5.38% | 80.17% | NA |
| Indica II | 465 | 9.00% | 32.50% | 5.38% | 53.12% | NA |
| Indica III | 913 | 6.90% | 0.00% | 12.49% | 80.61% | NA |
| Indica Intermediate | 786 | 11.70% | 4.10% | 10.05% | 74.17% | NA |
| Temperate Japonica | 767 | 97.90% | 0.10% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 95.80% | 0.00% | 0.40% | 3.77% | NA |
| Japonica Intermediate | 241 | 88.00% | 0.40% | 0.00% | 11.62% | NA |
| VI/Aromatic | 96 | 64.60% | 0.00% | 4.17% | 31.25% | NA |
| Intermediate | 90 | 50.00% | 3.30% | 3.33% | 43.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0805870856 | C -> T | LOC_Os08g10120.1 | missense_variant ; p.Glu643Lys; MODERATE | nonsynonymous_codon ; E643K | Average:23.154; most accessible tissue: Minghui63 panicle, score: 46.754 | benign  |
0.677 |
DELETERIOUS | 0.04 |
| vg0805870856 | C -> DEL | LOC_Os08g10120.1 | N | frameshift_variant | Average:23.154; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805870856 | NA | 6.23E-08 | mr1082 | 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 |
| vg0805870856 | 4.99E-06 | NA | mr1083 | 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 |
| vg0805870856 | 5.53E-07 | 1.89E-07 | mr1083 | 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 |
| vg0805870856 | NA | 2.16E-07 | mr1226 | 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 |
| vg0805870856 | NA | 8.26E-09 | mr1410 | 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 |
| vg0805870856 | 1.12E-06 | 8.87E-09 | mr1411 | 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 |
| vg0805870856 | NA | 7.61E-07 | mr1599 | 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 |