Search for Variation information by Variation ID:
Detailed information for vg0503273281:
| Variant ID: vg0503273281 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 3273281 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTTATTGGAGATTTTAATGAAACCCTTTGGCAGTTCGAGCACTTCTCAAAAAACCCACGTTGTGAAACTCAGATGCAGAATTTTCGTGATGCCTTATAT[G/C]
ACTGTGATTTACAGGATTTAGGCTTCAAAGGGGTTCCGCATACATATGACAATAGAAGAGATGGATGGAGAAATGTGAAGGTCAGGTTGGATAGAGCAGT
Reverse complement sequence
ACTGCTCTATCCAACCTGACCTTCACATTTCTCCATCCATCTCTTCTATTGTCATATGTATGCGGAACCCCTTTGAAGCCTAAATCCTGTAAATCACAGT[C/G]
ATATAAGGCATCACGAAAATTCTGCATCTGAGTTTCACAACGTGGGTTTTTTGAGAAGTGCTCGAACTGCCAAAGGGTTTCATTAAAATCTCCAATAACC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.30% | 4.10% | 1.48% | 61.15% | NA |
| All Indica | 2759 | 4.80% | 0.10% | 2.21% | 92.86% | NA |
| All Japonica | 1512 | 84.90% | 12.40% | 0.33% | 2.31% | NA |
| Aus | 269 | 5.60% | 0.00% | 0.37% | 94.05% | NA |
| Indica I | 595 | 2.00% | 0.00% | 2.18% | 95.80% | NA |
| Indica II | 465 | 5.80% | 0.00% | 1.29% | 92.90% | NA |
| Indica III | 913 | 5.70% | 0.20% | 1.86% | 92.22% | NA |
| Indica Intermediate | 786 | 5.30% | 0.10% | 3.18% | 91.35% | NA |
| Temperate Japonica | 767 | 87.60% | 9.90% | 0.52% | 1.96% | NA |
| Tropical Japonica | 504 | 86.70% | 10.90% | 0.20% | 2.18% | NA |
| Japonica Intermediate | 241 | 72.60% | 23.70% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 61.10% | 2.20% | 2.22% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503273281 | G -> DEL | LOC_Os05g06390.1 | N | frameshift_variant | Average:6.544; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0503273281 | G -> C | LOC_Os05g06390.1 | missense_variant ; p.Asp803His; MODERATE | nonsynonymous_codon ; D803H | Average:6.544; most accessible tissue: Zhenshan97 root, score: 12.891 | probably damaging  |
2.548 |
TOLERATED | 0.64 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0503273281 | 3.33E-06 | 2.79E-06 | mr1860 | Jap_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 |
| vg0503273281 | NA | 1.26E-06 | mr1051_2 | Jap_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 |