Search for Variation information by Variation ID:
Detailed information for vg1111678675:
| Variant ID: vg1111678675 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 11678675 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
ATGGTTGGAATTGATAAAAGATTACGACATGGGGATACACTACCATCCAGGCAAGGCTAATGTAGTAGCAGACGCTCTGAGCAGGAAAAGCTACTGCAAC[G/A]
CCTTGGGTATTGGAGACATGAGTGACAAGTTGCTACAAGAGCTTGAACCCCTCAACTTAGGAATTGTAGAACACGGGTACGTGGCTGCCCTTGAGGCACA
Reverse complement sequence
TGTGCCTCAAGGGCAGCCACGTACCCGTGTTCTACAATTCCTAAGTTGAGGGGTTCAAGCTCTTGTAGCAACTTGTCACTCATGTCTCCAATACCCAAGG[C/T]
GTTGCAGTAGCTTTTCCTGCTCAGAGCGTCTGCTACTACATTAGCCTTGCCTGGATGGTAGTGTATCCCCATGTCGTAATCTTTTATCAATTCCAACCAT
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 | 87.30% | 11.20% | 1.50% | 0.00% | NA |
| All Indica | 2759 | 94.30% | 4.90% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 83.40% | 15.50% | 1.12% | 0.00% | NA |
| Aus | 269 | 34.20% | 56.10% | 9.67% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 0.90% | 1.08% | 0.00% | NA |
| Indica III | 913 | 87.50% | 11.90% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 2.30% | 1.53% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 53.60% | 43.80% | 2.58% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.40% | 5.00% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 5.60% | 6.67% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1111678675 | G -> A | LOC_Os11g20220.1 | missense_variant ; p.Ala611Thr; MODERATE | nonsynonymous_codon ; A611T | Average:52.44; most accessible tissue: Minghui63 young leaf, score: 68.07 | possibly damaging  |
1.757 |
TOLERATED | 0.24 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1111678675 | NA | 2.94E-06 | mr1125 | 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 |
| vg1111678675 | 2.24E-06 | NA | mr1386 | 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 |
| vg1111678675 | NA | 5.52E-07 | mr1422 | 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 |
| vg1111678675 | NA | 2.82E-06 | mr1578 | 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 |
| vg1111678675 | NA | 4.43E-10 | mr1696 | 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 |
| vg1111678675 | NA | 5.10E-07 | mr1295_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 |
| vg1111678675 | NA | 9.69E-08 | mr1642_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 |