Search for Variation information by Variation ID:
Detailed information for vg0142473201:
| Variant ID: vg0142473201 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42473201 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 92. )
Flanking Sequence (100 bp) in Reference Genome:
GGCAACACTAGCAATCTATTCTGGCATTATCTCTCTTTCGCTACTTTGTGTGAAGCTATTCAAGGATGGTGTGCTGCAGACGAAGATTAGGGACAAAGAC[G/A]
ATCCCCGCCTGTCCAAGATGCGGAAAGAGGTGGTGGCTGGGGGAAAGGATACTATGGAGGTGGACAATGACTTCTTCCTGGTGCCTGTCAAGATCTCTGA
Reverse complement sequence
TCAGAGATCTTGACAGGCACCAGGAAGAAGTCATTGTCCACCTCCATAGTATCCTTTCCCCCAGCCACCACCTCTTTCCGCATCTTGGACAGGCGGGGAT[C/T]
GTCTTTGTCCCTAATCTTCGTCTGCAGCACACCATCCTTGAATAGCTTCACACAAAGTAGCGAAAGAGAGATAATGCCAGAATAGATTGCTAGTGTTGCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.80% | 46.40% | 0.68% | 2.07% | NA |
| All Indica | 2759 | 64.80% | 34.50% | 0.65% | 0.07% | NA |
| All Japonica | 1512 | 19.60% | 73.50% | 0.73% | 6.22% | NA |
| Aus | 269 | 80.30% | 19.30% | 0.37% | 0.00% | NA |
| Indica I | 595 | 86.90% | 12.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 31.20% | 66.90% | 1.51% | 0.43% | NA |
| Indica III | 913 | 65.90% | 33.60% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 66.50% | 32.80% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 33.10% | 66.80% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 3.40% | 76.80% | 1.98% | 17.86% | NA |
| Japonica Intermediate | 241 | 10.40% | 88.00% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 72.90% | 26.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 37.80% | 58.90% | 1.11% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142473201 | G -> A | LOC_Os01g73280.1 | missense_variant ; p.Asp117Asn; MODERATE | nonsynonymous_codon ; D117N | Average:46.565; most accessible tissue: Zhenshan97 flag leaf, score: 76.925 | benign  |
0.614 |
TOLERATED | 0.07 |
| vg0142473201 | G -> DEL | LOC_Os01g73280.1 | N | frameshift_variant | Average:46.565; most accessible tissue: Zhenshan97 flag leaf, score: 76.925 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0142473201 | NA | 2.24E-06 | mr1171 | 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 |
| vg0142473201 | 1.77E-06 | NA | mr1968 | 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 |
| vg0142473201 | 1.05E-06 | 2.01E-09 | mr1974 | 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 |
| vg0142473201 | 3.10E-06 | 4.29E-11 | mr1974 | 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 |
| vg0142473201 | NA | 1.78E-06 | mr1188_2 | 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 |