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Detailed information for vg0414059978:

Variant ID: vg0414059978 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14059978
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTTTTGGTGAGTTATGTACTCCATTCAATTTCACCATGCAGAAAAAGAAAATTAAAAAAAAAGTAAATAATGTACTAGCAAAGCATGCATAACCATCG[G/T]
CTGCCTCATTATTTAGGTATCGTCATTGGACTTAGTGCTGGCTTTGGAATTCTACTGCCTGGCTTAAGCGCAAAAATGCTCTTCCATAAATGGAAGAAAG

Reverse complement sequence

CTTTCTTCCATTTATGGAAGAGCATTTTTGCGCTTAAGCCAGGCAGTAGAATTCCAAAGCCAGCACTAAGTCCAATGACGATACCTAAATAATGAGGCAG[C/A]
CGATGGTTATGCATGCTTTGCTAGTACATTATTTACTTTTTTTTTAATTTTCTTTTTCTGCATGGTGAAATTGAATGGAGTACATAACTCACCAAAAAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.60% 19.30% 0.11% 0.00% NA
All Indica  2759 68.30% 31.50% 0.14% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 90.30% 9.70% 0.00% 0.00% NA
Indica I  595 63.20% 36.80% 0.00% 0.00% NA
Indica II  465 90.50% 9.50% 0.00% 0.00% NA
Indica III  913 63.20% 36.80% 0.00% 0.00% NA
Indica Intermediate  786 65.00% 34.50% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg0414059978 G -> T LOC_Os04g24510.1 intron_variant ; MODIFIER silent_mutation Average:49.57; most accessible tissue: Callus, score: 72.115 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414059978 NA 8.07E-08 mr1037 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
vg0414059978 NA 2.82E-09 mr1066 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
vg0414059978 NA 2.20E-08 mr1066 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
vg0414059978 NA 1.87E-06 mr1094 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
vg0414059978 NA 7.25E-06 mr1131 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
vg0414059978 NA 4.02E-06 mr1192 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
vg0414059978 NA 3.93E-06 mr1216 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
vg0414059978 NA 8.34E-06 mr1216 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
vg0414059978 NA 7.47E-06 mr1404 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
vg0414059978 NA 2.54E-06 mr1705 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
vg0414059978 NA 5.71E-06 mr1835 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
vg0414059978 NA 9.54E-06 mr1655_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