Search for Variation information by Variation ID:
Detailed information for vg0617642038:
| Variant ID: vg0617642038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 17642038 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 51. )
Flanking Sequence (100 bp) in Reference Genome:
GTCATGCGACCGGTCTGACCGAGCCATCAGGCCGGTCTGACCGTGCTCCGGATGTCGGTCTGACCGGCGCGTCTGGCCGGTCTGACCAGTGGTCTATGGC[T/C]
GGCCTGACCGGGCTCCAGCGCCGGTTTGACAGGAGGATTGCAAAGGGCGATGTGGAAGCTTCATCGTCTTCAAACAAAGTTAATACAGGGCATTATTTAC
Reverse complement sequence
GTAAATAATGCCCTGTATTAACTTTGTTTGAAGACGATGAAGCTTCCACATCGCCCTTTGCAATCCTCCTGTCAAACCGGCGCTGGAGCCCGGTCAGGCC[A/G]
GCCATAGACCACTGGTCAGACCGGCCAGACGCGCCGGTCAGACCGACATCCGGAGCACGGTCAGACCGGCCTGATGGCTCGGTCAGACCGGTCGCATGAC
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 | 38.30% | 7.20% | 7.70% | 46.87% | NA |
| All Indica | 2759 | 9.40% | 9.30% | 8.88% | 72.49% | NA |
| All Japonica | 1512 | 96.80% | 0.40% | 0.26% | 2.51% | NA |
| Aus | 269 | 16.00% | 3.30% | 32.71% | 47.96% | NA |
| Indica I | 595 | 15.60% | 7.10% | 6.72% | 70.59% | NA |
| Indica II | 465 | 10.50% | 3.70% | 1.94% | 83.87% | NA |
| Indica III | 913 | 3.40% | 13.60% | 13.36% | 69.66% | NA |
| Indica Intermediate | 786 | 10.80% | 9.30% | 9.41% | 70.48% | NA |
| Temperate Japonica | 767 | 96.10% | 0.00% | 0.13% | 3.78% | NA |
| Tropical Japonica | 504 | 98.60% | 0.40% | 0.40% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.40% | 1.70% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 5.20% | 60.40% | 19.79% | 14.58% | NA |
| Intermediate | 90 | 42.20% | 11.10% | 8.89% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0617642038 | T -> C | LOC_Os06g30510.1 | synonymous_variant ; p.Ala577Ala; LOW | synonymous_codon | Average:14.949; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0617642038 | T -> C | LOC_Os06g30510.1 | synonymous_variant ; p.Ala577Ala; LOW | nonsynonymous_codon ; A577V | Average:14.949; most accessible tissue: Zhenshan97 panicle, score: 36.038 | benign  |
1.412 |
TOLERATED | 0.09 |
| vg0617642038 | T -> DEL | LOC_Os06g30510.1 | N | frameshift_variant | Average:14.949; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617642038 | 2.06E-06 | NA | mr1078 | 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 |
| vg0617642038 | 1.02E-06 | 2.23E-10 | mr1078 | 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 |
| vg0617642038 | NA | 7.30E-06 | mr1200 | 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 |
| vg0617642038 | 4.52E-06 | NA | mr1078_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 |
| vg0617642038 | NA | 3.24E-08 | mr1078_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 |
| vg0617642038 | 7.51E-06 | NA | mr1108_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 |