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Detailed information for vg0113945497:

Variant ID: vg0113945497 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13945497
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CCGGGAGGCTACACCCTCCCTCTCTATATATACCCGAGGTATGAAGCCTAAAGCCACGAACCAATCTTGTACAAGTCGTCCTAATCTCCTAGGAAACCTT[C/T]
CCGTACAAGAAACAAACTTTACAAACTCCAATTGTATCAAATTTGGACTCCCACCAAATTCAACTCCGCATCCCATACGCATATAATATCTCCATCGTAT

Reverse complement sequence

ATACGATGGAGATATTATATGCGTATGGGATGCGGAGTTGAATTTGGTGGGAGTCCAAATTTGATACAATTGGAGTTTGTAAAGTTTGTTTCTTGTACGG[G/A]
AAGGTTTCCTAGGAGATTAGGACGACTTGTACAAGATTGGTTCGTGGCTTTAGGCTTCATACCTCGGGTATATATAGAGAGGGAGGGTGTAGCCTCCCGG

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 94.90% 5.10% 0.02% 0.00% NA
All Indica  2759 92.80% 7.20% 0.04% 0.00% NA
All Japonica  1512 97.30% 2.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.00% 16.00% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 89.80% 10.10% 0.13% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0113945497 C -> T LOC_Os01g24780.1 downstream_gene_variant ; 806.0bp to feature; MODIFIER silent_mutation Average:42.759; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0113945497 C -> T LOC_Os01g24780-LOC_Os01g24790 intergenic_region ; MODIFIER silent_mutation Average:42.759; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113945497 7.88E-06 1.11E-07 mr1064 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
vg0113945497 3.83E-06 2.42E-08 mr1136 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
vg0113945497 NA 4.09E-06 mr1316 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
vg0113945497 NA 7.24E-06 mr1671 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
vg0113945497 NA 6.37E-06 mr1679 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
vg0113945497 NA 4.71E-06 mr1693 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
vg0113945497 6.69E-06 5.71E-08 mr1741 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