Search for Variation information by Variation ID:
Detailed information for vg1126042091:
| Variant ID: vg1126042091 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26042091 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
ACAGGAAATATGGGAACTGGACTATGGCCTGAACATCCAGATCCTTGTGCTCCGTTGTGAATGGGTTAAAGACACAATAGGAGTTTCCGTTGATGACTAC[G/A]
GGCTAACAATAGTCGATCACAGTAAAACAGGCCACAAGGATGATCCATGGGTTTTAGCAGAGCGTGTGGCTCAAGTGTTTTATGTGAAGGACCCTTCGGA
Reverse complement sequence
TCCGAAGGGTCCTTCACATAAAACACTTGAGCCACACGCTCTGCTAAAACCCATGGATCATCCTTGTGGCCTGTTTTACTGTGATCGACTATTGTTAGCC[C/T]
GTAGTCATCAACGGAAACTCCTATTGTGTCTTTAACCCATTCACAACGGAGCACAAGGATCTGGATGTTCAGGCCATAGTCCAGTTCCCATATTTCCTGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.10% | 8.40% | 2.01% | 0.51% | NA |
| All Indica | 2759 | 88.80% | 9.50% | 0.80% | 0.87% | NA |
| All Japonica | 1512 | 86.70% | 8.50% | 4.76% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.30% | 1.01% | 0.00% | NA |
| Indica II | 465 | 94.80% | 4.70% | 0.22% | 0.22% | NA |
| Indica III | 913 | 78.20% | 19.70% | 0.00% | 2.08% | NA |
| Indica Intermediate | 786 | 90.10% | 7.50% | 1.91% | 0.51% | NA |
| Temperate Japonica | 767 | 82.70% | 10.40% | 6.91% | 0.00% | NA |
| Tropical Japonica | 504 | 95.80% | 4.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 80.50% | 12.00% | 7.47% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1126042091 | G -> A | LOC_Os11g43150.1 | missense_variant ; p.Gly625Arg; MODERATE | nonsynonymous_codon ; G625R | Average:31.427; most accessible tissue: Minghui63 young leaf, score: 51.901 | probably damaging  |
2.607 |
DELETERIOUS | 0.02 |
| vg1126042091 | G -> DEL | LOC_Os11g43150.1 | N | frameshift_variant | Average:31.427; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126042091 | NA | 6.73E-06 | mr1006 | 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 |
| vg1126042091 | 9.56E-06 | 3.04E-07 | mr1007 | 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 |
| vg1126042091 | 7.31E-06 | NA | mr1624 | 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 |