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Detailed information for vg0204429559:

Variant ID: vg0204429559 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4429559
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCATCTCGTATACACAAGTTTTTAGAAATCTGTAGAAATCTTGCAATGGAATTGGGAGAGGGCCTGAAACTTGATGTGACCACAAGATGGAGTTCAAC[T/C]
TATCATATGTTGAGAACTTGCATTGCATATCAGCAAGCATTAGATTCATATGCAGAAACAGATTTAAATTATGAGTGGAAGCCCAGCCCAGAAGAGTGGG

Reverse complement sequence

CCCACTCTTCTGGGCTGGGCTTCCACTCATAATTTAAATCTGTTTCTGCATATGAATCTAATGCTTGCTGATATGCAATGCAAGTTCTCAACATATGATA[A/G]
GTTGAACTCCATCTTGTGGTCACATCAAGTTTCAGGCCCTCTCCCAATTCCATTGCAAGATTTCTACAGATTTCTAAAAACTTGTGTATACGAGATGGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.50% 8.10% 10.01% 24.33% NA
All Indica  2759 46.90% 13.10% 11.78% 28.23% NA
All Japonica  1512 72.50% 0.30% 5.29% 21.96% NA
Aus  269 70.60% 4.80% 15.24% 9.29% NA
Indica I  595 40.50% 33.60% 14.79% 11.09% NA
Indica II  465 37.40% 3.00% 12.04% 47.53% NA
Indica III  913 52.40% 7.60% 11.50% 28.59% NA
Indica Intermediate  786 51.00% 9.90% 9.67% 29.39% NA
Temperate Japonica  767 97.70% 0.10% 0.52% 1.69% NA
Tropical Japonica  504 37.30% 0.60% 12.50% 49.60% NA
Japonica Intermediate  241 66.00% 0.00% 5.39% 28.63% NA
VI/Aromatic  96 74.00% 0.00% 18.75% 7.29% NA
Intermediate  90 75.60% 6.70% 10.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204429559 T -> DEL LOC_Os02g08340.1 N frameshift_variant Average:22.325; most accessible tissue: Zhenshan97 root, score: 41.416 N N N N
vg0204429559 T -> C LOC_Os02g08340.1 synonymous_variant ; p.Thr474Thr; LOW synonymous_codon Average:22.325; most accessible tissue: Zhenshan97 root, score: 41.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204429559 2.28E-06 NA mr1191 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
vg0204429559 NA 9.04E-07 mr1191 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
vg0204429559 1.47E-07 NA mr1644 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
vg0204429559 9.78E-07 9.11E-08 mr1644 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
vg0204429559 9.77E-12 NA mr1191_2 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
vg0204429559 2.04E-10 3.07E-09 mr1191_2 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