Search for Variation information by Variation ID:
Detailed information for vg0100695213:
| Variant ID: vg0100695213 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 695213 |
| Reference Allele: G | Alternative Allele: C,A |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, C: 0.00, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
CCTTTCTGCGTCCTGGGTAAGCCAACTACAAAGTCCATACCAATCTCATCCCATTTCCACACTGGGATGGGTAGAGGTTGTAATAATCCAGCTAGCTTCC[G/C,A]
ATGTTCCGCTTTAATCCTTTGACAAGTATCGCAATGAGCGACAAACTGCGCAATGTCGGCTTTCATCCCATTCCACCAATATTTCTGCTTTATATCCATA
Reverse complement sequence
TATGGATATAAAGCAGAAATATTGGTGGAATGGGATGAAAGCCGACATTGCGCAGTTTGTCGCTCATTGCGATACTTGTCAAAGGATTAAAGCGGAACAT[C/G,T]
GGAAGCTAGCTGGATTATTACAACCTCTACCCATCCCAGTGTGGAAATGGGATGAGATTGGTATGGACTTTGTAGTTGGCTTACCCAGGACGCAGAAAGG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.60% | 9.50% | 1.35% | 14.54% | NA |
| All Indica | 2759 | 94.10% | 1.10% | 0.36% | 4.49% | NA |
| All Japonica | 1512 | 45.50% | 19.90% | 2.05% | 32.54% | NA |
| Aus | 269 | 49.40% | 30.10% | 4.09% | 16.36% | NA |
| Indica I | 595 | 96.00% | 0.00% | 0.34% | 3.70% | NA |
| Indica II | 465 | 95.50% | 2.20% | 0.00% | 2.37% | NA |
| Indica III | 913 | 94.70% | 0.10% | 0.44% | 4.71% | NA |
| Indica Intermediate | 786 | 91.10% | 2.30% | 0.51% | 6.11% | NA |
| Temperate Japonica | 767 | 70.40% | 21.60% | 0.78% | 7.17% | NA |
| Tropical Japonica | 504 | 9.10% | 13.50% | 3.57% | 73.81% | NA |
| Japonica Intermediate | 241 | 42.30% | 27.80% | 2.90% | 26.97% | NA |
| VI/Aromatic | 96 | 43.80% | 28.10% | 7.29% | 20.83% | NA |
| Intermediate | 90 | 74.40% | 12.20% | 5.56% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100695213 | G -> A | LOC_Os01g02260.1 | missense_variant ; p.Arg230Trp; MODERATE | N | Average:37.42; most accessible tissue: Minghui63 root, score: 60.831 | N | N | N | N |
| vg0100695213 | G -> A | LOC_Os01g02250.1 | downstream_gene_variant ; 1200.0bp to feature; MODIFIER | N | Average:37.42; most accessible tissue: Minghui63 root, score: 60.831 | N | N | N | N |
| vg0100695213 | G -> DEL | LOC_Os01g02260.1 | N | frameshift_variant | Average:37.42; most accessible tissue: Minghui63 root, score: 60.831 | N | N | N | N |
| vg0100695213 | G -> C | LOC_Os01g02260.1 | missense_variant ; p.Arg230Gly; MODERATE | nonsynonymous_codon ; R230G | Average:37.42; most accessible tissue: Minghui63 root, score: 60.831 | benign  |
1.275 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100695213 | 3.25E-07 | NA | Grain_weight | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0100695213 | 4.70E-06 | NA | mr1336 | 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 |
| vg0100695213 | 2.03E-06 | 2.03E-06 | mr1336 | 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 |