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Detailed information for vg0630964914:

Variant ID: vg0630964914 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30964914
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


TCGTTAGATCTAATAATGCTCATCTTGCCAGCTAGATCCAACGATCGTAAATGTTTTGGTACCGTGAGATATCGGTACCTTAAGGTATTTTTTATTGGAC[C/T]
GGAGAAAATTACGTATTAATATCTTGTACACAATGTAGGTGAGATCCCGGCAGTTTGAGGAGATGCATACCTTCGACCGCAGAATTGCCAGCGCCGACAA

Reverse complement sequence

TTGTCGGCGCTGGCAATTCTGCGGTCGAAGGTATGCATCTCCTCAAACTGCCGGGATCTCACCTACATTGTGTACAAGATATTAATACGTAATTTTCTCC[G/A]
GTCCAATAAAAAATACCTTAAGGTACCGATATCTCACGGTACCAAAACATTTACGATCGTTGGATCTAGCTGGCAAGATGAGCATTATTAGATCTAACGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.70% 6.40% 5.84% 0.00% NA
All Indica  2759 80.00% 10.70% 9.31% 0.00% NA
All Japonica  1512 99.30% 0.10% 0.60% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 61.70% 23.00% 15.29% 0.00% NA
Indica II  465 82.40% 5.80% 11.83% 0.00% NA
Indica III  913 93.80% 3.60% 2.63% 0.00% NA
Indica Intermediate  786 76.60% 12.30% 11.07% 0.00% NA
Temperate Japonica  767 99.00% 0.00% 1.04% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 2.10% 1.04% 0.00% NA
Intermediate  90 84.40% 6.70% 8.89% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0630964914 C -> T LOC_Os06g51190.1 upstream_gene_variant ; 2405.0bp to feature; MODIFIER silent_mutation Average:52.31; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0630964914 C -> T LOC_Os06g51180.1 intron_variant ; MODIFIER silent_mutation Average:52.31; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630964914 3.45E-06 2.39E-11 mr1038 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
vg0630964914 9.26E-06 5.19E-12 mr1038 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
vg0630964914 6.23E-08 2.95E-14 mr1389 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
vg0630964914 1.54E-06 4.26E-13 mr1389 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
vg0630964914 1.50E-07 1.59E-14 mr1038_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
vg0630964914 7.40E-07 1.21E-13 mr1038_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
vg0630964914 2.30E-07 2.00E-12 mr1389_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
vg0630964914 1.70E-06 1.46E-12 mr1389_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