Search for Variation information by Variation ID:
Detailed information for vg0804076961:
| Variant ID: vg0804076961 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4076961 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
ATATCCTCGGAACTCATGAAAACTTGAATTGCAGCACAAAAGCTAACTCCAGAGGCCACCAGGCAATCCCTAGAAAAGGCTGATGACTTGAGAACAGTCA[G/T,A]
TATCGTCCTAACAACATGCTTGAAGACAGTAGATGCTTTGTCAAGTTCAGTAAACTTAGAAGGGTAGCGCTGCAGCAAGTAGTACATGCAAGACATAGCC
Reverse complement sequence
GGCTATGTCTTGCATGTACTACTTGCTGCAGCGCTACCCTTCTAAGTTTACTGAACTTGACAAAGCATCTACTGTCTTCAAGCATGTTGTTAGGACGATA[C/A,T]
TGACTGTTCTCAAGTCATCAGCCTTTTCTAGGGATTGCCTGGTGGCCTCTGGAGTTAGCTTTTGTGCTGCAATTCAAGTTTTCATGAGTTCCGAGGATAT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.60% | 1.50% | 0.93% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.00% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 92.90% | 4.60% | 2.51% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 90.10% | 5.60% | 4.30% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 9.10% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804076961 | G -> T | LOC_Os08g07290.1 | missense_variant ; p.Leu235Met; MODERATE | nonsynonymous_codon ; L235M | Average:62.861; most accessible tissue: Callus, score: 83.768 | probably damaging  |
2.14 |
TOLERATED | 0.07 |
| vg0804076961 | G -> A | LOC_Os08g07290.1 | synonymous_variant ; p.Leu235Leu; LOW | N | Average:62.861; most accessible tissue: Callus, score: 83.768 | N | N | N | N |
| vg0804076961 | G -> A | LOC_Os08g07300.1 | upstream_gene_variant ; 1704.0bp to feature; MODIFIER | N | Average:62.861; most accessible tissue: Callus, score: 83.768 | N | N | N | N |
| vg0804076961 | G -> A | LOC_Os08g07290.2 | upstream_gene_variant ; 847.0bp to feature; MODIFIER | N | Average:62.861; most accessible tissue: Callus, score: 83.768 | N | N | N | N |
| vg0804076961 | G -> A | LOC_Os08g07300.2 | upstream_gene_variant ; 1704.0bp to feature; MODIFIER | N | Average:62.861; most accessible tissue: Callus, score: 83.768 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0804076961 | 6.21E-06 | NA | mr1031 | 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 |
| vg0804076961 | 1.83E-06 | NA | mr1056 | 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 |
| vg0804076961 | 7.50E-07 | 7.50E-07 | mr1197_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 |
| vg0804076961 | 1.22E-06 | 5.95E-06 | mr1546_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 |