Search for Variation information by Variation ID:
Detailed information for vg0417353746:
| Variant ID: vg0417353746 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17353746 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 49. )
Flanking Sequence (100 bp) in Reference Genome:
ACCCCAGGCCGCATCAAGAGAATACACCTGCAACCAGTGATGGACAAGTTGCAATCAAGGTTAGCGGGATGGAAAGGGAAGTTAATCCAGCAATCAGGGC[G/A]
GAAGACGCTAGTCACGTCTATTTTCAGCTCCATACCAACCTACTTCCTTACCACCTTAAAGCCGCCTAAACAGTTCCTCACAGACATGGACAAGATTAGG
Reverse complement sequence
CCTAATCTTGTCCATGTCTGTGAGGAACTGTTTAGGCGGCTTTAAGGTGGTAAGGAAGTAGGTTGGTATGGAGCTGAAAATAGACGTGACTAGCGTCTTC[C/T]
GCCCTGATTGCTGGATTAACTTCCCTTTCCATCCCGCTAACCTTGATTGCAACTTGTCCATCACTGGTTGCAGGTGTATTCTCTTGATGCGGCCTGGGGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.20% | 4.80% | 2.94% | 5.06% | NA |
| All Indica | 2759 | 87.40% | 8.10% | 2.72% | 1.85% | NA |
| All Japonica | 1512 | 89.30% | 0.00% | 2.05% | 8.66% | NA |
| Aus | 269 | 75.10% | 0.00% | 4.83% | 20.07% | NA |
| Indica I | 595 | 85.20% | 3.70% | 5.88% | 5.21% | NA |
| Indica II | 465 | 68.00% | 27.50% | 3.66% | 0.86% | NA |
| Indica III | 913 | 98.80% | 0.10% | 0.44% | 0.66% | NA |
| Indica Intermediate | 786 | 87.20% | 9.20% | 2.42% | 1.27% | NA |
| Temperate Japonica | 767 | 81.90% | 0.00% | 3.13% | 14.99% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 91.30% | 0.00% | 2.49% | 6.22% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 19.79% | 1.04% | NA |
| Intermediate | 90 | 92.20% | 4.40% | 1.11% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417353746 | G -> DEL | LOC_Os04g29270.1 | N | frameshift_variant | Average:39.921; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0417353746 | G -> A | LOC_Os04g29270.1 | missense_variant ; p.Arg1147Gln; MODERATE | nonsynonymous_codon ; R1147Q | Average:39.921; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | possibly damaging  |
1.549 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417353746 | NA | 3.51E-06 | mr1851 | 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 |
| vg0417353746 | 2.67E-06 | 4.70E-08 | mr1864 | Ind_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 |