Search for Variation information by Variation ID:
Detailed information for vg0318523246:
| Variant ID: vg0318523246 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18523246 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.24, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
TTGAGAGCTTGCGCTCTTGATTTTGGTGGAGCTTGGGATAAAAGCTTGCCATATGCGGAATTCTCGTACAACAACAGCTACCAGGCCAGTCTACAGATGG[T/C]
ACCGTTTGAAGCTTTATACGGCCGGAAGTGCCGCACACCTCTCTTCTGGGATCAGGCAGGCGAGCGTCAACTGTTCGGGATAGAGGTATTAGCGGAAGCA
Reverse complement sequence
TGCTTCCGCTAATACCTCTATCCCGAACAGTTGACGCTCGCCTGCCTGATCCCAGAAGAGAGGTGTGCGGCACTTCCGGCCGTATAAAGCTTCAAACGGT[A/G]
CCATCTGTAGACTGGCCTGGTAGCTGTTGTTGTACGAGAATTCCGCATATGGCAAGCTTTTATCCCAAGCTCCACCAAAATCAAGAGCGCAAGCTCTCAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.20% | 10.00% | 22.62% | 35.25% | NA |
| All Indica | 2759 | 4.00% | 13.10% | 27.04% | 55.82% | NA |
| All Japonica | 1512 | 84.10% | 6.30% | 8.73% | 0.86% | NA |
| Aus | 269 | 9.70% | 0.70% | 57.25% | 32.34% | NA |
| Indica I | 595 | 3.20% | 7.40% | 41.01% | 48.40% | NA |
| Indica II | 465 | 4.90% | 5.80% | 20.00% | 69.25% | NA |
| Indica III | 913 | 2.00% | 23.40% | 22.02% | 52.57% | NA |
| Indica Intermediate | 786 | 6.50% | 9.80% | 26.46% | 57.25% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 60.90% | 13.50% | 23.61% | 1.98% | NA |
| Japonica Intermediate | 241 | 83.00% | 11.20% | 4.98% | 0.83% | NA |
| VI/Aromatic | 96 | 71.90% | 6.20% | 20.83% | 1.04% | NA |
| Intermediate | 90 | 46.70% | 6.70% | 18.89% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318523246 | T -> C | LOC_Os03g32380.1 | missense_variant ; p.Val719Ala; MODERATE | nonsynonymous_codon ; V719A | Average:11.666; most accessible tissue: Callus, score: 28.814 | possibly damaging  |
-1.565 |
TOLERATED | 1.00 |
| vg0318523246 | T -> DEL | LOC_Os03g32380.1 | N | frameshift_variant | Average:11.666; most accessible tissue: Callus, score: 28.814 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0318523246 | NA | 5.62E-06 | mr1215 | 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 |
| vg0318523246 | NA | 1.41E-08 | mr1718 | Ind_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 |
| vg0318523246 | 1.53E-07 | 4.97E-18 | mr1750 | Ind_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 |
| vg0318523246 | 1.71E-06 | 1.71E-06 | mr1849 | 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 |
| vg0318523246 | NA | 1.12E-11 | mr1718_2 | Ind_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 |
| vg0318523246 | 1.94E-07 | 1.40E-25 | mr1750_2 | Ind_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 |