Search for Variation information by Variation ID:
Detailed information for vg0335714781:
| Variant ID: vg0335714781 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35714781 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, C: 0.32, others allele: 0.00, population size: 38. )
Flanking Sequence (100 bp) in Reference Genome:
ATCTCTTGGCAATGTCACCAACCATTTTGAGTAGCTCAGGAGGCCTTTCTTGTTCTGAACTGAAAGCACTTGTCTTGATAATTTCCTCTATGAAGCTTTC[A/C]
TTCAGTCTCTTGAGATCATAAGCTTTTTGAGCTGGAGCCATCACTTGAGCAACTGCTTGATCACGAGTTGTTGTCAACACTGAGCTACCGCTGCCACCAT
Reverse complement sequence
ATGGTGGCAGCGGTAGCTCAGTGTTGACAACAACTCGTGATCAAGCAGTTGCTCAAGTGATGGCTCCAGCTCAAAAAGCTTATGATCTCAAGAGACTGAA[T/G]
GAAAGCTTCATAGAGGAAATTATCAAGACAAGTGCTTTCAGTTCAGAACAAGAAAGGCCTCCTGAGCTACTCAAAATGGTTGGTGACATTGCCAAGAGAT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.00% | 18.30% | 0.74% | 61.96% | NA |
| All Indica | 2759 | 27.70% | 2.20% | 1.01% | 69.12% | NA |
| All Japonica | 1512 | 0.50% | 51.80% | 0.26% | 47.49% | NA |
| Aus | 269 | 39.40% | 0.00% | 0.74% | 59.85% | NA |
| Indica I | 595 | 23.70% | 3.00% | 1.68% | 71.60% | NA |
| Indica II | 465 | 15.50% | 4.50% | 1.72% | 78.28% | NA |
| Indica III | 913 | 39.60% | 0.30% | 0.33% | 59.69% | NA |
| Indica Intermediate | 786 | 23.90% | 2.40% | 0.89% | 72.77% | NA |
| Temperate Japonica | 767 | 0.10% | 86.60% | 0.13% | 13.17% | NA |
| Tropical Japonica | 504 | 0.80% | 6.00% | 0.40% | 92.86% | NA |
| Japonica Intermediate | 241 | 0.80% | 36.90% | 0.41% | 61.83% | NA |
| VI/Aromatic | 96 | 6.20% | 2.10% | 1.04% | 90.62% | NA |
| Intermediate | 90 | 17.80% | 21.10% | 0.00% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0335714781 | A -> C | LOC_Os03g63200.1 | missense_variant ; p.Asn332Lys; MODERATE | nonsynonymous_codon | Average:25.768; most accessible tissue: Callus, score: 73.09 | benign  |
-0.026 |
TOLERATED | 0.45 |
| vg0335714781 | A -> DEL | LOC_Os03g63200.1 | N | frameshift_variant | Average:25.768; most accessible tissue: Callus, score: 73.09 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0335714781 | NA | 2.61E-06 | mr1182 | 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 |
| vg0335714781 | 1.76E-06 | 1.75E-06 | mr1440_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 |
| vg0335714781 | NA | 1.86E-07 | mr1794_2 | 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 |
| vg0335714781 | NA | 2.29E-06 | mr1851_2 | 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 |