Search for Variation information by Variation ID:
Detailed information for vg1209219626:
| Variant ID: vg1209219626 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9219626 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.81, G: 0.19, others allele: 0.00, population size: 105. )
Flanking Sequence (100 bp) in Reference Genome:
GCTCTGATTCCCGAAGATTTGGCCGATGTCCTAACTCCAGCCGCTTATCTCGAGCAACATCAGTTCAAGCTGGAAAAAGCCAAGCTAAGACTAGTCGAAC[A/G]
CCGTGAGCGCAAAGAGATTGAGGCCGCAATCCAAGCTAATCGGCAGCTTGTGCATGAAGAGAAGACCAAACTTGATCAGCTATCTGAAGGTCCGATCAAA
Reverse complement sequence
TTTGATCGGACCTTCAGATAGCTGATCAAGTTTGGTCTTCTCTTCATGCACAAGCTGCCGATTAGCTTGGATTGCGGCCTCAATCTCTTTGCGCTCACGG[T/C]
GTTCGACTAGTCTTAGCTTGGCTTTTTCCAGCTTGAACTGATGTTGCTCGAGATAAGCGGCTGGAGTTAGGACATCGGCCAAATCTTCGGGAATCAGAGC
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 | 36.20% | 15.00% | 20.55% | 28.23% | NA |
| All Indica | 2759 | 6.70% | 23.60% | 30.48% | 39.22% | NA |
| All Japonica | 1512 | 94.80% | 0.70% | 1.12% | 3.44% | NA |
| Aus | 269 | 4.80% | 13.40% | 33.83% | 47.96% | NA |
| Indica I | 595 | 4.50% | 29.90% | 23.19% | 42.35% | NA |
| Indica II | 465 | 14.00% | 21.90% | 26.45% | 37.63% | NA |
| Indica III | 913 | 4.50% | 20.40% | 38.88% | 36.25% | NA |
| Indica Intermediate | 786 | 6.70% | 23.40% | 28.63% | 41.22% | NA |
| Temperate Japonica | 767 | 94.40% | 0.40% | 0.39% | 4.82% | NA |
| Tropical Japonica | 504 | 94.00% | 1.40% | 2.18% | 2.38% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.24% | 1.24% | NA |
| VI/Aromatic | 96 | 28.10% | 3.10% | 11.46% | 57.29% | NA |
| Intermediate | 90 | 56.70% | 13.30% | 12.22% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209219626 | A -> DEL | LOC_Os12g16140.1 | N | frameshift_variant | Average:31.736; most accessible tissue: Minghui63 flag leaf, score: 46.761 | N | N | N | N |
| vg1209219626 | A -> G | LOC_Os12g16140.1 | missense_variant ; p.His647Arg; MODERATE | nonsynonymous_codon ; H647R | Average:31.736; most accessible tissue: Minghui63 flag leaf, score: 46.761 | benign  |
-0.336 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209219626 | NA | 1.53E-07 | mr1425 | 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 |
| vg1209219626 | 7.97E-07 | NA | mr1425_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 |
| vg1209219626 | NA | 1.45E-08 | mr1425_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 |