Search for Variation information by Variation ID:
Detailed information for vg0334098522:
| Variant ID: vg0334098522 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098522 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, C: 0.31, others allele: 0.00, population size: 241. )
Flanking Sequence (100 bp) in Reference Genome:
AACTATTATCTTCTTGCAGCCGAAGTGGGTTAGCGGGACGACGCGTCGTGTGTACACACAGTTCGTAGCTGATTTTGATCAGCTTACGTCTAACCGTGTT[C/T]
GGTGGACTCCCTACACTCAGCACGATGACAATGATCGTGCACCACTCGGTCTCATGAACCTTTGCATGCGAGATATGCAACTCTGGAGGACTACTTGTCA
Reverse complement sequence
TGACAAGTAGTCCTCCAGAGTTGCATATCTCGCATGCAAAGGTTCATGAGACCGAGTGGTGCACGATCATTGTCATCGTGCTGAGTGTAGGGAGTCCACC[G/A]
AACACGGTTAGACGTAAGCTGATCAAAATCAGCTACGAACTGTGTGTACACACGACGCGTCGTCCCGCTAACCCACTTCGGCTGCAAGAAGATAATAGTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.50% | 45.90% | 0.19% | 0.47% | NA |
| All Indica | 2759 | 81.10% | 18.00% | 0.25% | 0.65% | NA |
| All Japonica | 1512 | 2.10% | 97.80% | 0.07% | 0.07% | NA |
| Aus | 269 | 79.60% | 20.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.70% | 12.80% | 0.00% | 0.50% | NA |
| Indica II | 465 | 91.80% | 7.30% | 0.22% | 0.65% | NA |
| Indica III | 913 | 70.00% | 29.20% | 0.11% | 0.66% | NA |
| Indica Intermediate | 786 | 83.50% | 15.10% | 0.64% | 0.76% | NA |
| Temperate Japonica | 767 | 0.50% | 99.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 5.20% | 94.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 5.20% | 93.80% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 42.20% | 54.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098522 | C -> T | LOC_Os03g59910.1 | missense_variant ; p.Arg51Trp; MODERATE | nonsynonymous_codon ; R51W | Average:47.05; most accessible tissue: Callus, score: 68.635 | probably damaging  |
3.422 |
DELETERIOUS | 0.00 |
| vg0334098522 | C -> DEL | LOC_Os03g59910.1 | N | frameshift_variant | Average:47.05; most accessible tissue: Callus, score: 68.635 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0334098522 | NA | 4.01E-10 | mr1249 | 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 |
| vg0334098522 | NA | 9.09E-06 | mr1098_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 |
| vg0334098522 | NA | 1.08E-08 | mr1198_2 | 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 |