Search for Variation information by Variation ID:
Detailed information for vg0710966151:
| Variant ID: vg0710966151 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10966151 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
TCCAACAAGTTTTAGATCGTCCAATTTAACATACTGACTTATCCTCGCTGAATAGCCCGATGGAACTTTAATATCCTTCAAGCATGATAACATTGCGATC[C/T]
TCTCATCCTTCGACAGTGTGTGGCAGGCTGGAGGGAGGTACACTTTACCTGTCTCTGCATCTCGTATGGGCTGGAGTTCGCTGCGAATATTCATGTCCTG
Reverse complement sequence
CAGGACATGAATATTCGCAGCGAACTCCAGCCCATACGAGATGCAGAGACAGGTAAAGTGTACCTCCCTCCAGCCTGCCACACACTGTCGAAGGATGAGA[G/A]
GATCGCAATGTTATCATGCTTGAAGGATATTAAAGTTCCATCGGGCTATTCAGCGAGGATAAGTCAGTATGTTAAATTGGACGATCTAAAACTTGTTGGA
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 | 26.30% | 0.10% | 12.31% | 61.26% | NA |
| All Indica | 2759 | 2.50% | 0.30% | 15.59% | 81.66% | NA |
| All Japonica | 1512 | 74.60% | 0.00% | 4.50% | 20.90% | NA |
| Aus | 269 | 1.10% | 0.00% | 24.54% | 74.35% | NA |
| Indica I | 595 | 2.00% | 1.00% | 30.92% | 66.05% | NA |
| Indica II | 465 | 4.70% | 0.00% | 9.25% | 86.02% | NA |
| Indica III | 913 | 1.80% | 0.00% | 6.24% | 92.00% | NA |
| Indica Intermediate | 786 | 2.40% | 0.10% | 18.58% | 78.88% | NA |
| Temperate Japonica | 767 | 65.80% | 0.00% | 0.52% | 33.64% | NA |
| Tropical Japonica | 504 | 85.90% | 0.00% | 12.30% | 1.79% | NA |
| Japonica Intermediate | 241 | 78.80% | 0.00% | 0.83% | 20.33% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 9.38% | 84.38% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 10.00% | 50.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710966151 | C -> DEL | LOC_Os07g18530.1 | N | frameshift_variant | Average:12.74; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0710966151 | C -> T | LOC_Os07g18530.1 | missense_variant ; p.Arg448Lys; MODERATE | nonsynonymous_codon ; R448K | Average:12.74; most accessible tissue: Zhenshan97 root, score: 16.934 | possibly damaging  |
-1.503 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0710966151 | 2.70E-06 | NA | mr1281_2 | 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 |
| vg0710966151 | NA | 1.30E-07 | mr1681_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 |
| vg0710966151 | NA | 4.47E-11 | mr1714_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 |
| vg0710966151 | 3.96E-07 | NA | mr1842_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 |
| vg0710966151 | NA | 9.37E-12 | mr1986_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 |