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Detailed information for vg0604638830:

Variant ID: vg0604638830 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4638830
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGTTTCGGTCAGAATTATCCGAAAATTCTTGCATTCGGAAACGAATTCGGATATTTTTTTTCTCGGAAACGAAAACGAAAACAGTAAGGGTACTATCC[G/A]
TCGGAATCGGAAAACGGTCGGAAATTATCCGGAATTTTTTTCGGATATCCGCAGAAATTGAGCAAATTATATAAAAAAACATGTATATATACATAACTTT

Reverse complement sequence

AAAGTTATGTATATATACATGTTTTTTTATATAATTTGCTCAATTTCTGCGGATATCCGAAAAAAATTCCGGATAATTTCCGACCGTTTTCCGATTCCGA[C/T]
GGATAGTACCCTTACTGTTTTCGTTTTCGTTTCCGAGAAAAAAAATATCCGAATTCGTTTCCGAATGCAAGAATTTTCGGATAATTCTGACCGAAACTAT

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 59.60% 40.40% 0.00% 0.00% NA
All Indica  2759 85.60% 14.40% 0.00% 0.00% NA
All Japonica  1512 22.00% 78.00% 0.00% 0.00% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 56.30% 43.70% 0.00% 0.00% NA
Indica III  913 95.10% 4.90% 0.00% 0.00% NA
Indica Intermediate  786 81.70% 18.30% 0.00% 0.00% NA
Temperate Japonica  767 3.30% 96.70% 0.00% 0.00% NA
Tropical Japonica  504 44.40% 55.60% 0.00% 0.00% NA
Japonica Intermediate  241 34.90% 65.10% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 47.80% 52.20% 0.00% 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
vg0604638830 G -> A LOC_Os06g09220.1 upstream_gene_variant ; 3361.0bp to feature; MODIFIER silent_mutation Average:23.527; most accessible tissue: Minghui63 root, score: 38.567 N N N N
vg0604638830 G -> A LOC_Os06g09230.2 downstream_gene_variant ; 1761.0bp to feature; MODIFIER silent_mutation Average:23.527; most accessible tissue: Minghui63 root, score: 38.567 N N N N
vg0604638830 G -> A LOC_Os06g09220-LOC_Os06g09230 intergenic_region ; MODIFIER silent_mutation Average:23.527; most accessible tissue: Minghui63 root, score: 38.567 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604638830 NA 7.47E-14 mr1141 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
vg0604638830 NA 8.52E-06 mr1189 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
vg0604638830 NA 5.30E-07 mr1629 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
vg0604638830 NA 2.48E-09 mr1860 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
vg0604638830 NA 8.89E-10 mr1903 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
vg0604638830 NA 7.36E-11 mr1907 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
vg0604638830 NA 9.10E-15 mr1141_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
vg0604638830 NA 2.01E-09 mr1660_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
vg0604638830 NA 5.27E-06 mr1667_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
vg0604638830 NA 1.81E-06 mr1695_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
vg0604638830 NA 4.02E-13 mr1860_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
vg0604638830 NA 8.76E-07 mr1860_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