Search for Variation information by Variation ID:
Detailed information for vg0142338439:
| Variant ID: vg0142338439 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42338439 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )
Flanking Sequence (100 bp) in Reference Genome:
CTGATAAAAGTGCTGGCAAATGTGGCAGACTTCTGCTCAACTAGTTGCTCACAGAGCATGTACAAACAGATGGCATAGCTACTCACCGGGGTACCCTTTA[T/C]
AACAGTTGACACATGACCAGGAGCAATCCCCTCTGATTCTGGCTCTGGGGCAAGCCGAGAGAGACCAAAATCAGCAACTTTTGCGACAAACTTTGAGTCC
Reverse complement sequence
GGACTCAAAGTTTGTCGCAAAAGTTGCTGATTTTGGTCTCTCTCGGCTTGCCCCAGAGCCAGAATCAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTT[A/G]
TAAAGGGTACCCCGGTGAGTAGCTATGCCATCTGTTTGTACATGCTCTGTGAGCAACTAGTTGAGCAGAAGTCTGCCACATTTGCCAGCACTTTTATCAG
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 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 86.60% | 13.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 75.50% | 24.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0142338439 | T -> C | LOC_Os01g72990.1 | missense_variant ; p.Ile778Val; MODERATE | nonsynonymous_codon ; I778V | Average:67.949; most accessible tissue: Callus, score: 85.235 | benign  |
-0.597 |
TOLERATED | 1.00 |
| vg0142338439 | T -> C | LOC_Os01g72990.2 | missense_variant ; p.Ile778Val; MODERATE | nonsynonymous_codon ; I778V | Average:67.949; most accessible tissue: Callus, score: 85.235 | benign |
-0.559 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0142338439 | 3.20E-07 | NA | mr1181_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 |
| vg0142338439 | 6.79E-06 | NA | mr1195_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 |
| vg0142338439 | 3.37E-06 | NA | mr1256_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 |
| vg0142338439 | 1.75E-06 | 1.75E-06 | mr1256_2 | 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 |