Search for Variation information by Variation ID:
Detailed information for vg0420967277:
| Variant ID: vg0420967277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967277 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCGGCGGCGGCGGAGGCGGAGGCGGCCCTCCTCCTCCTCGTCGGGCGTCCCCGCATCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTAC[T/G]
TCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCGCCCCGAGCGCTCGCTTTGCAATCACCGGCACCACCTTTGAATTTTTTTTCTATATGG
Reverse complement sequence
CCATATAGAAAAAAAATTCAAAGGTGGTGCCGGTGATTGCAAAGCGAGCGCTCGGGGCGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGA[A/C]
GTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGATGCGGGGACGCCCGACGAGGAGGAGGAGGGCCGCCTCCGCCTCCGCCGCCGCCGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.80% | 0.10% | 9.88% | 35.25% | NA |
| All Indica | 2759 | 37.20% | 0.10% | 8.41% | 54.30% | NA |
| All Japonica | 1512 | 91.70% | 0.10% | 1.46% | 6.81% | NA |
| Aus | 269 | 24.20% | 0.00% | 69.89% | 5.95% | NA |
| Indica I | 595 | 77.30% | 0.00% | 0.50% | 22.18% | NA |
| Indica II | 465 | 14.80% | 0.40% | 3.87% | 80.86% | NA |
| Indica III | 913 | 29.70% | 0.00% | 15.01% | 55.31% | NA |
| Indica Intermediate | 786 | 28.60% | 0.30% | 9.41% | 61.70% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 78.60% | 0.20% | 3.97% | 17.26% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.83% | 6.22% | NA |
| VI/Aromatic | 96 | 54.20% | 0.00% | 15.62% | 30.21% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 11.11% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967277 | T -> DEL | LOC_Os04g34670.1 | N | frameshift_variant | Average:32.621; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0420967277 | T -> G | LOC_Os04g34670.1 | missense_variant ; p.Phe14Val; MODERATE | nonsynonymous_codon ; F14V | Average:32.621; most accessible tissue: Zhenshan97 panicle, score: 52.263 | possibly damaging  |
-1.663 |
TOLERATED | 0.31 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0420967277 | NA | 2.37E-09 | Heading_date | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0420967277 | NA | 3.40E-10 | mr1714 | 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 |