Search for Variation information by Variation ID:
Detailed information for vg1118850288:
| Variant ID: vg1118850288 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18850288 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 117. )
Flanking Sequence (100 bp) in Reference Genome:
CAACTGGTGGACTCTACAGCCGGCTGTGAGCTGTTGAGCTTTCTCGACGCTTACTCCGGCTACCACCAAATCAGCATGGCAAAAGAGGACGAAGAGAAGA[C/T]
AACATTCATCATGCCATTCGGGGTATTTTGCTATGTTAAGATGTCGTTCGGATTGATAACAGCAGGGAATACTTTCCAGCGCACGGTCCAGGGCGCACTT
Reverse complement sequence
AAGTGCGCCCTGGACCGTGCGCTGGAAAGTATTCCCTGCTGTTATCAATCCGAACGACATCTTAACATAGCAAAATACCCCGAATGGCATGATGAATGTT[G/A]
TCTTCTCTTCGTCCTCTTTTGCCATGCTGATTTGGTGGTAGCCGGAGTAAGCGTCGAGAAAGCTCAACAGCTCACAGCCGGCTGTAGAGTCCACCAGTTG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.50% | 30.50% | 1.06% | 0.00% | NA |
| All Indica | 2759 | 54.30% | 44.50% | 1.23% | 0.00% | NA |
| All Japonica | 1512 | 96.40% | 3.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 70.60% | 24.90% | 4.46% | 0.00% | NA |
| Indica I | 595 | 69.70% | 29.70% | 0.50% | 0.00% | NA |
| Indica II | 465 | 67.10% | 32.30% | 0.65% | 0.00% | NA |
| Indica III | 913 | 39.30% | 58.70% | 1.97% | 0.00% | NA |
| Indica Intermediate | 786 | 52.30% | 46.40% | 1.27% | 0.00% | NA |
| Temperate Japonica | 767 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 28.10% | 68.80% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 71.10% | 28.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1118850288 | C -> T | LOC_Os11g31990.1 | missense_variant ; p.Thr763Ile; MODERATE | nonsynonymous_codon ; T763I | Average:22.692; most accessible tissue: Callus, score: 27.118 | benign  |
0.683 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118850288 | NA | 6.68E-06 | mr1837 | 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 |
| vg1118850288 | NA | 2.76E-06 | mr1958 | 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 |
| vg1118850288 | 3.39E-06 | NA | mr1200_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 |