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Detailed information for vg0103243222:

Variant ID: vg0103243222 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3243222
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATATTAGAGTATCGTACGAAAGCAAGTATAAAATCGCTCTATCAGGATAATACGGCTGTCACTTACAAAGGGAACACTCTTATGTTCACTAAAATCCT[G/A,T]
ACCACCTTCAAAGCAATTGATCTCTCAGACAACTCATTTGGTGGTCCTATTCCAAAGTCAATGGGGGAAGCTTGCTTCACTACATGGATTTAACCTGTCC

Reverse complement sequence

GGACAGGTTAAATCCATGTAGTGAAGCAAGCTTCCCCCATTGACTTTGGAATAGGACCACCAAATGAGTTGTCTGAGAGATCAATTGCTTTGAAGGTGGT[C/T,A]
AGGATTTTAGTGAACATAAGAGTGTTCCCTTTGTAAGTGACAGCCGTATTATCCTGATAGAGCGATTTTATACTTGCTTTCGTACGATACTCTAATATTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.00% 0.60% 0.51% 10.30% T: 0.57%
All Indica  2759 98.00% 0.00% 0.14% 1.12% T: 0.69%
All Japonica  1512 67.50% 1.80% 0.79% 29.70% T: 0.26%
Aus  269 96.70% 0.00% 2.23% 0.00% T: 1.12%
Indica I  595 98.70% 0.00% 0.00% 1.34% NA
Indica II  465 98.90% 0.00% 0.00% 1.08% NA
Indica III  913 97.30% 0.00% 0.22% 0.99% T: 1.53%
Indica Intermediate  786 98.00% 0.00% 0.25% 1.15% T: 0.64%
Temperate Japonica  767 92.80% 1.70% 0.52% 4.95% NA
Tropical Japonica  504 30.80% 2.40% 1.19% 65.08% T: 0.60%
Japonica Intermediate  241 63.50% 0.80% 0.83% 34.44% T: 0.41%
VI/Aromatic  96 97.90% 0.00% 1.04% 0.00% T: 1.04%
Intermediate  90 90.00% 1.10% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103243222 G -> T LOC_Os01g06836.1 synonymous_variant ; p.Leu490Leu; LOW synonymous_codon Average:54.713; most accessible tissue: Callus, score: 78.93 N N N N
vg0103243222 G -> A LOC_Os01g06836.1 synonymous_variant ; p.Leu490Leu; LOW synonymous_codon Average:54.713; most accessible tissue: Callus, score: 78.93 N N N N
vg0103243222 G -> DEL LOC_Os01g06836.1 N frameshift_variant Average:54.713; most accessible tissue: Callus, score: 78.93 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103243222 3.86E-06 3.86E-06 mr1054 Jap_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
vg0103243222 NA 2.60E-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
vg0103243222 NA 3.49E-07 mr1192 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
vg0103243222 NA 2.20E-06 mr1280 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
vg0103243222 NA 1.92E-07 mr1289 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
vg0103243222 NA 1.27E-06 mr1338 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
vg0103243222 5.87E-06 5.87E-06 mr1372 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
vg0103243222 NA 3.84E-08 mr1779 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
vg0103243222 NA 7.65E-13 mr1900 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
vg0103243222 1.08E-06 1.08E-06 mr1972 Jap_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
vg0103243222 NA 4.31E-18 mr1945_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