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Detailed information for vg0517887964:

Variant ID: vg0517887964 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17887964
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, C: 0.28, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CTTACTAGCTCCCAAACAAGCCATTTGACTAAAATGTTCACTCTATGCCCATAAATATGGCACACTTTAGTGAGATGCAGATGCAGTTAATTTCAGAATC[C/T]
AATAGGAGTAACAGAAAGTACCACCAAACATTGAAGGAGACACCGAAAGAATCCAGACAACATACAAACACATGAGGAACAATTAAGACCAACACAGTTC

Reverse complement sequence

GAACTGTGTTGGTCTTAATTGTTCCTCATGTGTTTGTATGTTGTCTGGATTCTTTCGGTGTCTCCTTCAATGTTTGGTGGTACTTTCTGTTACTCCTATT[G/A]
GATTCTGAAATTAACTGCATCTGCATCTCACTAAAGTGTGCCATATTTATGGGCATAGAGTGAACATTTTAGTCAAATGGCTTGTTTGGGAGCTAGTAAG

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 64.70% 35.10% 0.23% 0.00% NA
All Indica  2759 94.10% 5.60% 0.25% 0.00% NA
All Japonica  1512 8.70% 91.20% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 74.40% 25.20% 0.43% 0.00% NA
Indica III  913 99.10% 0.50% 0.33% 0.00% NA
Indica Intermediate  786 95.50% 4.20% 0.25% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 20.00% 79.80% 0.20% 0.00% NA
Japonica Intermediate  241 2.90% 96.70% 0.41% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 53.30% 44.40% 2.22% 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
vg0517887964 C -> T LOC_Os05g30830.1 downstream_gene_variant ; 4005.0bp to feature; MODIFIER silent_mutation Average:64.001; most accessible tissue: Callus, score: 83.529 N N N N
vg0517887964 C -> T LOC_Os05g30820.1 intron_variant ; MODIFIER silent_mutation Average:64.001; most accessible tissue: Callus, score: 83.529 N N N N
vg0517887964 C -> T LOC_Os05g30820.2 intron_variant ; MODIFIER silent_mutation Average:64.001; most accessible tissue: Callus, score: 83.529 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517887964 NA 9.34E-07 mr1044 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
vg0517887964 NA 7.16E-07 mr1044 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
vg0517887964 NA 2.92E-12 mr1069 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
vg0517887964 NA 3.56E-06 mr1077 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
vg0517887964 NA 3.03E-18 mr1133 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
vg0517887964 NA 1.73E-29 mr1202 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
vg0517887964 NA 5.25E-06 mr1415 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
vg0517887964 NA 6.89E-06 mr1482 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
vg0517887964 NA 5.25E-06 mr1567 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
vg0517887964 NA 1.28E-16 mr1842 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
vg0517887964 NA 2.41E-12 mr1902 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
vg0517887964 NA 9.17E-06 mr1002_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
vg0517887964 NA 1.36E-37 mr1072_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
vg0517887964 NA 5.56E-07 mr1654_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
vg0517887964 NA 7.13E-10 mr1756_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