Search for Variation information by Variation ID:
Detailed information for vg0334098510:
| Variant ID: vg0334098510 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098510 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.10, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
ATAACTAATCATAACTATTATCTTCTTGCAGCCGAAGTGGGTTAGCGGGACGACGCGTCGTGTGTACACACAGTTCGTAGCTGATTTTGATCAGCTTACG[T/C]
CTAACCGTGTTCGGTGGACTCCCTACACTCAGCACGATGACAATGATCGTGCACCACTCGGTCTCATGAACCTTTGCATGCGAGATATGCAACTCTGGAG
Reverse complement sequence
CTCCAGAGTTGCATATCTCGCATGCAAAGGTTCATGAGACCGAGTGGTGCACGATCATTGTCATCGTGCTGAGTGTAGGGAGTCCACCGAACACGGTTAG[A/G]
CGTAAGCTGATCAAAATCAGCTACGAACTGTGTGTACACACGACGCGTCGTCCCGCTAACCCACTTCGGCTGCAAGAAGATAATAGTTATGATTAGTTAT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.10% | 45.20% | 0.21% | 0.42% | NA |
| All Indica | 2759 | 82.10% | 17.00% | 0.33% | 0.58% | NA |
| All Japonica | 1512 | 2.10% | 97.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 79.90% | 20.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.70% | 12.80% | 0.00% | 0.50% | NA |
| Indica II | 465 | 93.80% | 5.60% | 0.22% | 0.43% | NA |
| Indica III | 913 | 71.40% | 27.80% | 0.11% | 0.66% | NA |
| Indica Intermediate | 786 | 84.10% | 14.40% | 0.89% | 0.64% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | 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 | 45.60% | 51.10% | 0.00% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098510 | T -> C | LOC_Os03g59910.1 | missense_variant ; p.Ser47Pro; MODERATE | nonsynonymous_codon ; S47P | Average:48.675; most accessible tissue: Callus, score: 68.635 | possibly damaging  |
-1.831 |
TOLERATED | 1.00 |
| vg0334098510 | T -> DEL | LOC_Os03g59910.1 | N | frameshift_variant | Average:48.675; 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 |
|---|---|---|---|---|---|---|
| vg0334098510 | NA | 7.82E-06 | mr1098 | 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 |
| vg0334098510 | 8.51E-06 | 8.25E-11 | 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 |
| vg0334098510 | NA | 5.63E-06 | mr1961 | 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 |
| vg0334098510 | NA | 3.43E-12 | mr1151_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 |
| vg0334098510 | NA | 2.46E-09 | 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 |
| vg0334098510 | NA | 1.39E-07 | mr1681_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 |