Search for Variation information by Variation ID:
Detailed information for vg0330523640:
| Variant ID: vg0330523640 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 30523640 |
| 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: 368. )
Flanking Sequence (100 bp) in Reference Genome:
GGTGCTTGCCATCCTCAACAATGACAAGATCAAGAGCCCTGAGAAGAAGAGGGGGATCGACAAGTTCCTCGACCCCATCTCCGACCAGATGTTCCACCAG[T/C]
TCGTCTCCATCGGTAAGCTCATCACAGATTTTCATGATACTGCAGTTTGTGATTCAGCTAGTGAACTGGATGAAAATTTCGGCGTTGCTGTTGAGTTTGA
Reverse complement sequence
TCAAACTCAACAGCAACGCCGAAATTTTCATCCAGTTCACTAGCTGAATCACAAACTGCAGTATCATGAAAATCTGTGATGAGCTTACCGATGGAGACGA[A/G]
CTGGTGGAACATCTGGTCGGAGATGGGGTCGAGGAACTTGTCGATCCCCCTCTTCTTCTCAGGGCTCTTGATCTTGTCATTGTTGAGGATGGCAAGCACC
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 | 91.90% | 5.60% | 2.52% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 75.70% | 16.70% | 7.61% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 56.60% | 30.20% | 13.17% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 0.40% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.00% | 7.50% | 4.56% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 8.90% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0330523640 | T -> C | LOC_Os03g53220.1 | missense_variant ; p.Phe190Leu; MODERATE | nonsynonymous_codon ; F190L | Average:67.343; most accessible tissue: Zhenshan97 root, score: 78.34 | benign  |
-0.318 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0330523640 | 3.98E-07 | 3.98E-07 | mr1779 | 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 |