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Detailed information for vg0126148298:

Variant ID: vg0126148298 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 26148298
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCTTCAAAAGGTTTTAAATTGTATCAAATGGATGTAAAAAGTACTTTTCTAAATGGTTTTATACAGGAGGAAGTTTATGTCAAACAACCACCAGGTTTT[A/G]
AAAATCCTGATTTTCCCAACCATGTTTTTAAATTGTCTAAAGCTTTGTATGGTTTGAAACAAGCTCCTAGGGCATGGTATGATAGGCTTAAGAACTTTTT

Reverse complement sequence

AAAAAGTTCTTAAGCCTATCATACCATGCCCTAGGAGCTTGTTTCAAACCATACAAAGCTTTAGACAATTTAAAAACATGGTTGGGAAAATCAGGATTTT[T/C]
AAAACCTGGTGGTTGTTTGACATAAACTTCCTCCTGTATAAAACCATTTAGAAAAGTACTTTTTACATCCATTTGATACAATTTAAAACCTTTTGAAGCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.20% 16.80% 4.04% 0.00% NA
All Indica  2759 95.00% 1.50% 3.52% 0.00% NA
All Japonica  1512 64.50% 34.10% 1.39% 0.00% NA
Aus  269 17.50% 57.60% 24.91% 0.00% NA
Indica I  595 96.00% 0.00% 4.03% 0.00% NA
Indica II  465 97.80% 1.50% 0.65% 0.00% NA
Indica III  913 94.90% 1.80% 3.40% 0.00% NA
Indica Intermediate  786 92.60% 2.40% 4.96% 0.00% NA
Temperate Japonica  767 95.00% 3.40% 1.56% 0.00% NA
Tropical Japonica  504 28.40% 70.80% 0.79% 0.00% NA
Japonica Intermediate  241 42.70% 55.20% 2.07% 0.00% NA
VI/Aromatic  96 32.30% 63.50% 4.17% 0.00% NA
Intermediate  90 75.60% 22.20% 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
vg0126148298 A -> G LOC_Os01g46000.1 missense_variant ; p.Lys1190Glu; MODERATE nonsynonymous_codon ; K1190E Average:15.736; most accessible tissue: Minghui63 flower, score: 23.1 benign -0.781 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0126148298 NA 5.99E-06 mr1338 Jap_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
vg0126148298 NA 1.76E-07 mr1530 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
vg0126148298 NA 6.46E-11 mr1696 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
vg0126148298 NA 7.89E-07 mr1756 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
vg0126148298 NA 1.65E-16 mr1180_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
vg0126148298 NA 1.54E-12 mr1189_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
vg0126148298 NA 9.48E-10 mr1449_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
vg0126148298 NA 6.89E-16 mr1530_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
vg0126148298 NA 2.77E-19 mr1552_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
vg0126148298 NA 8.71E-08 mr1642_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
vg0126148298 NA 1.04E-07 mr1696_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
vg0126148298 NA 9.72E-07 mr1730_2 Jap_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
vg0126148298 NA 3.43E-06 mr1762_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
vg0126148298 NA 2.83E-06 mr1866_2 Jap_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
vg0126148298 NA 3.85E-12 mr1942_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
vg0126148298 NA 1.29E-06 mr1966_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