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Detailed information for vg0429946087:

Variant ID: vg0429946087 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29946087
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, C: 0.29, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CGCTCCTGCTAAGGCCCAAGTTTTGGCCTCTTCCTTGATCTTGGCTAAAAGAGAGATAGCTGAAAGCTCCTTCTGTTGGAAGGTTCTGCGATTCCTTTCG[C/T]
TCCATATCTCCCAGGCGACCAACAACATCAAAGTGCGGAGTGCCTTCTTAGATGTCTCTTGTATGTTTGCGGTAGCCTCCCACCAATCTAGCACCGTTGA

Reverse complement sequence

TCAACGGTGCTAGATTGGTGGGAGGCTACCGCAAACATACAAGAGACATCTAAGAAGGCACTCCGCACTTTGATGTTGTTGGTCGCCTGGGAGATATGGA[G/A]
CGAAAGGAATCGCAGAACCTTCCAACAGAAGGAGCTTTCAGCTATCTCTCTTTTAGCCAAGATCAAGGAAGAGGCCAAAACTTGGGCCTTAGCAGGAGCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.80% 24.60% 0.06% 0.53% NA
All Indica  2759 63.60% 35.60% 0.07% 0.76% NA
All Japonica  1512 99.60% 0.30% 0.00% 0.13% NA
Aus  269 45.00% 55.00% 0.00% 0.00% NA
Indica I  595 81.20% 18.50% 0.17% 0.17% NA
Indica II  465 29.70% 69.00% 0.00% 1.29% NA
Indica III  913 65.50% 34.00% 0.00% 0.55% NA
Indica Intermediate  786 68.10% 30.70% 0.13% 1.15% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.00% 0.20% NA
Japonica Intermediate  241 98.30% 1.20% 0.00% 0.41% NA
VI/Aromatic  96 94.80% 4.20% 1.04% 0.00% NA
Intermediate  90 72.20% 25.60% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0429946087 C -> DEL LOC_Os04g50188.1 N frameshift_variant Average:51.941; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0429946087 C -> T LOC_Os04g50188.1 missense_variant ; p.Ser68Asn; MODERATE nonsynonymous_codon ; S68N Average:51.941; most accessible tissue: Zhenshan97 panicle, score: 67.02 benign -1.205 TOLERATED 0.58

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429946087 NA 6.81E-06 mr1138 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
vg0429946087 3.52E-06 6.08E-13 mr1169 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
vg0429946087 5.78E-08 6.75E-18 mr1174 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
vg0429946087 7.60E-12 8.76E-23 mr1174 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
vg0429946087 NA 6.84E-08 mr1347 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
vg0429946087 2.11E-06 2.38E-12 mr1347 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
vg0429946087 NA 6.65E-09 mr1354 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
vg0429946087 NA 2.50E-07 mr1406 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
vg0429946087 NA 4.59E-06 mr1531 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
vg0429946087 NA 3.80E-06 mr1138_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
vg0429946087 1.68E-06 3.42E-14 mr1174_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
vg0429946087 1.49E-11 2.61E-24 mr1174_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
vg0429946087 1.51E-06 1.23E-09 mr1347_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
vg0429946087 9.92E-10 6.72E-21 mr1347_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
vg0429946087 NA 2.33E-10 mr1354_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
vg0429946087 NA 1.51E-08 mr1406_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
vg0429946087 NA 7.24E-07 mr1540_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
vg0429946087 NA 8.17E-07 mr1732_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