Search for Variation information by Variation ID:
Detailed information for vg1106572640:
| Variant ID: vg1106572640 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 6572640 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 34. )
Flanking Sequence (100 bp) in Reference Genome:
AAAGAAACGCCATGTAATGACTCGGCTGACAAGGAGATTCAGCCAGAAAACACCGTGCCGCAGGAGTACTGCGACACACTGTTGCTGCCATTCCCCCAGC[G/A]
GAGTAGGAAACCGTCAGTGGACAAGCAGTTCGCTTGTTTTGTTGAAGTGATCCAAAAGATCCACATCAACGTGCCGTCATTGGACGCTATGCAAGTGCCA
Reverse complement sequence
TGGCACTTGCATAGCGTCCAATGACGGCACGTTGATGTGGATCTTTTGGATCACTTCAACAAAACAAGCGAACTGCTTGTCCACTGACGGTTTCCTACTC[C/T]
GCTGGGGGAATGGCAGCAACAGTGTGTCGCAGTACTCCTGCGGCACGGTGTTTTCTGGCTGAATCTCCTTGTCAGCCGAGTCATTACATGGCGTTTCTTT
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 | 48.70% | 35.10% | 5.48% | 10.71% | NA |
| All Indica | 2759 | 54.70% | 29.50% | 6.63% | 9.24% | NA |
| All Japonica | 1512 | 41.80% | 39.10% | 3.97% | 15.15% | NA |
| Aus | 269 | 18.60% | 74.70% | 2.97% | 3.72% | NA |
| Indica I | 595 | 67.40% | 24.50% | 4.71% | 3.36% | NA |
| Indica II | 465 | 44.90% | 28.40% | 12.90% | 13.76% | NA |
| Indica III | 913 | 53.50% | 32.00% | 3.83% | 10.73% | NA |
| Indica Intermediate | 786 | 52.20% | 30.90% | 7.63% | 9.29% | NA |
| Temperate Japonica | 767 | 33.40% | 45.60% | 4.69% | 16.30% | NA |
| Tropical Japonica | 504 | 55.60% | 29.20% | 2.98% | 12.30% | NA |
| Japonica Intermediate | 241 | 39.80% | 39.00% | 3.73% | 17.43% | NA |
| VI/Aromatic | 96 | 70.80% | 24.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 46.70% | 36.70% | 7.78% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1106572640 | G -> A | LOC_Os11g11840.1 | missense_variant ; p.Arg201Gln; MODERATE | nonsynonymous_codon ; R201Q | Average:11.071; most accessible tissue: Callus, score: 28.416 | benign  |
0.76 |
TOLERATED | 0.08 |
| vg1106572640 | G -> DEL | LOC_Os11g11840.1 | N | frameshift_variant | Average:11.071; most accessible tissue: Callus, score: 28.416 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1106572640 | 4.45E-06 | NA | mr1199 | 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 |