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Detailed information for vg0402103921:

Variant ID: vg0402103921 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2103921
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGAGATCAACATAATAGCAACAGAGTCCCGCGACTTTGGAATAGATGGCATTATATTACCTGTCTATCAGTTGGAAGACCTTGTCAAAAACCTTCTCCT[T/C]
TTTATTCATTGAGTCGTACACAGTGACTCTGCATGCGTCCAAGTCGAAAAAGAACAGGACCAGTGGAATCTAGAATATGCGTGAGATGAGATAAATATCA

Reverse complement sequence

TGATATTTATCTCATCTCACGCATATTCTAGATTCCACTGGTCCTGTTCTTTTTCGACTTGGACGCATGCAGAGTCACTGTGTACGACTCAATGAATAAA[A/G]
AGGAGAAGGTTTTTGACAAGGTCTTCCAACTGATAGACAGGTAATATAATGCCATCTATTCCAAAGTCGCGGGACTCTGTTGCTATTATGTTGATCTCGG

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 50.30% 0.30% 2.26% 47.06% NA
All Indica  2759 43.00% 0.60% 2.43% 54.01% NA
All Japonica  1512 56.50% 0.00% 0.86% 42.59% NA
Aus  269 87.40% 0.00% 6.32% 6.32% NA
Indica I  595 42.70% 0.00% 3.19% 54.12% NA
Indica II  465 20.20% 0.20% 1.51% 78.06% NA
Indica III  913 52.90% 1.40% 2.63% 43.04% NA
Indica Intermediate  786 45.20% 0.30% 2.16% 52.42% NA
Temperate Japonica  767 87.00% 0.00% 0.26% 12.78% NA
Tropical Japonica  504 24.20% 0.00% 1.59% 74.21% NA
Japonica Intermediate  241 27.40% 0.00% 1.24% 71.37% NA
VI/Aromatic  96 57.30% 0.00% 8.33% 34.38% NA
Intermediate  90 53.30% 0.00% 2.22% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402103921 T -> C LOC_Os04g04420.1 missense_variant ; p.Lys567Glu; MODERATE nonsynonymous_codon ; K567E Average:7.907; most accessible tissue: Zhenshan97 panicle, score: 20.424 benign -0.008 TOLERATED 0.52
vg0402103921 T -> DEL LOC_Os04g04420.1 N frameshift_variant Average:7.907; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402103921 NA 6.17E-06 mr1006 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
vg0402103921 NA 1.31E-07 mr1030 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
vg0402103921 NA 8.54E-08 mr1045 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
vg0402103921 NA 2.19E-06 mr1285 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
vg0402103921 NA 1.46E-06 mr1311 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
vg0402103921 3.79E-06 9.61E-07 mr1339 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
vg0402103921 NA 7.04E-06 mr1432 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
vg0402103921 NA 2.82E-06 mr1576 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
vg0402103921 NA 6.82E-08 mr1666 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
vg0402103921 NA 1.90E-06 mr1727 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
vg0402103921 NA 8.76E-06 mr1928 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
vg0402103921 NA 3.04E-06 mr1965 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