Search for Variation information by Variation ID:
Detailed information for vg0403320747:
| Variant ID: vg0403320747 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3320747 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
AGCCGCTCAAGATCGTGAAGACCGGAATAGGGGGAAGATCTGCAAGCTAGAAGACAAGGTGGATCATTTGGAGAAGGAGCTAGCCGCGTTGAAGGGAGAA[G/T]
CACCACCGCAGAAGGCCAGAGTCCGTCTTACCGCAAGGAAGAGAGCTCTATTCGTCCCTCGCTATCAGTTGGCACCAAAGGTTCGTGTGGTGGAAAAAGA
Reverse complement sequence
TCTTTTTCCACCACACGAACCTTTGGTGCCAACTGATAGCGAGGGACGAATAGAGCTCTCTTCCTTGCGGTAAGACGGACTCTGGCCTTCTGCGGTGGTG[C/A]
TTCTCCCTTCAACGCGGCTAGCTCCTTCTCCAAATGATCCACCTTGTCTTCTAGCTTGCAGATCTTCCCCCTATTCCGGTCTTCACGATCTTGAGCGGCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.90% | 6.90% | 5.82% | 12.36% | NA |
| All Indica | 2759 | 69.70% | 7.90% | 6.09% | 16.35% | NA |
| All Japonica | 1512 | 93.30% | 0.30% | 2.12% | 4.30% | NA |
| Aus | 269 | 31.20% | 27.50% | 22.68% | 18.59% | NA |
| Indica I | 595 | 62.20% | 8.10% | 8.91% | 20.84% | NA |
| Indica II | 465 | 82.40% | 1.30% | 4.09% | 12.26% | NA |
| Indica III | 913 | 65.30% | 11.00% | 5.37% | 18.40% | NA |
| Indica Intermediate | 786 | 72.90% | 8.10% | 5.98% | 12.98% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.65% | 1.96% | NA |
| Tropical Japonica | 504 | 89.10% | 0.20% | 3.77% | 6.94% | NA |
| Japonica Intermediate | 241 | 89.20% | 1.20% | 3.32% | 6.22% | NA |
| VI/Aromatic | 96 | 57.30% | 24.00% | 11.46% | 7.29% | NA |
| Intermediate | 90 | 75.60% | 8.90% | 3.33% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403320747 | G -> DEL | LOC_Os04g06360.1 | N | frameshift_variant | Average:43.994; most accessible tissue: Minghui63 young leaf, score: 71.839 | N | N | N | N |
| vg0403320747 | G -> T | LOC_Os04g06360.1 | missense_variant ; p.Ala535Ser; MODERATE | nonsynonymous_codon ; A535S | Average:43.994; most accessible tissue: Minghui63 young leaf, score: 71.839 | benign  |
1.247 |
TOLERATED | 0.11 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403320747 | NA | 4.05E-06 | mr1008 | 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 |
| vg0403320747 | NA | 8.81E-06 | mr1009 | 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 |
| vg0403320747 | 2.08E-06 | 3.20E-06 | mr1011 | 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 |
| vg0403320747 | 4.78E-06 | 4.77E-06 | mr1012 | 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 |
| vg0403320747 | NA | 6.30E-07 | mr1008_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 |