Search for Variation information by Variation ID:
Detailed information for vg0416147172:
| Variant ID: vg0416147172 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 16147172 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGTGGACCGGTCCCTCCTAGCAGCTTTGGTCGACCGATGGAGGCCAGAGACGCACACTTTTCACTTGCCGTGCGGTGAGGTAGCCCCTACCCTACAGGAC[A/G,C]
TATCGTACTTGTTGGGGCTACCGCTCGCGGGAGACGCTGTTAGGCCAGTGACCACGGGTGTGGACTGGCAGGACGATCTTACGGCACGTTTCGCACTAGT
Reverse complement sequence
ACTAGTGCGAAACGTGCCGTAAGATCGTCCTGCCAGTCCACACCCGTGGTCACTGGCCTAACAGCGTCTCCCGCGAGCGGTAGCCCCAACAAGTACGATA[T/C,G]
GTCCTGTAGGGTAGGGGCTACCTCACCGCACGGCAAGTGAAAAGTGTGCGTCTCTGGCCTCCATCGGTCGACCAAAGCTGCTAGGAGGGACCGGTCCACA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.80% | 22.20% | 2.52% | 10.50% | NA |
| All Indica | 2759 | 73.30% | 13.90% | 1.92% | 10.91% | NA |
| All Japonica | 1512 | 62.00% | 37.20% | 0.26% | 0.46% | NA |
| Aus | 269 | 11.20% | 1.50% | 21.19% | 66.17% | NA |
| Indica I | 595 | 90.40% | 0.30% | 1.18% | 8.07% | NA |
| Indica II | 465 | 75.10% | 10.10% | 2.80% | 12.04% | NA |
| Indica III | 913 | 57.00% | 27.90% | 2.08% | 13.03% | NA |
| Indica Intermediate | 786 | 78.10% | 10.20% | 1.78% | 9.92% | NA |
| Temperate Japonica | 767 | 67.00% | 32.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 46.00% | 52.40% | 0.60% | 0.99% | NA |
| Japonica Intermediate | 241 | 79.70% | 19.50% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 14.60% | 76.00% | 3.12% | 6.25% | NA |
| Intermediate | 90 | 64.40% | 28.90% | 2.22% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0416147172 | A -> C | LOC_Os04g27320.1 | missense_variant ; p.Ile427Leu; MODERATE | N | Average:60.184; most accessible tissue: Zhenshan97 flag leaf, score: 83.526 | N | N | N | N |
| vg0416147172 | A -> C | LOC_Os04g27330.1 | downstream_gene_variant ; 2766.0bp to feature; MODIFIER | N | Average:60.184; most accessible tissue: Zhenshan97 flag leaf, score: 83.526 | N | N | N | N |
| vg0416147172 | A -> C | LOC_Os04g27340.1 | downstream_gene_variant ; 4467.0bp to feature; MODIFIER | N | Average:60.184; most accessible tissue: Zhenshan97 flag leaf, score: 83.526 | N | N | N | N |
| vg0416147172 | A -> DEL | LOC_Os04g27320.1 | N | frameshift_variant | Average:60.184; most accessible tissue: Zhenshan97 flag leaf, score: 83.526 | N | N | N | N |
| vg0416147172 | A -> G | LOC_Os04g27320.1 | missense_variant ; p.Ile427Val; MODERATE | nonsynonymous_codon ; I427V | Average:60.184; most accessible tissue: Zhenshan97 flag leaf, score: 83.526 | benign  |
-0.472 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0416147172 | NA | 1.18E-08 | mr1514 | 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 |
| vg0416147172 | 2.10E-06 | 2.09E-06 | mr1954 | 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 |