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Detailed information for vg0500670256:

Variant ID: vg0500670256 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 670256
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


TTATACCCCACAGAAACTATTTAATTATTAGACTTGGGAGCAAGTGTTTTACAAAAGCCTCACATACTTTCAAATATTTAAGAAAGGACAGGGCTGGAAG[C/G]
TCTCTAGTCCACATCGATCATATGGCACATTCCTAGAATTGCTTAACTTTTTTTTTTAGAAACTTGTGAAGTTGTGATTCAGTATTTAGGACATGTTTAA

Reverse complement sequence

TTAAACATGTCCTAAATACTGAATCACAACTTCACAAGTTTCTAAAAAAAAAAGTTAAGCAATTCTAGGAATGTGCCATATGATCGATGTGGACTAGAGA[G/C]
CTTCCAGCCCTGTCCTTTCTTAAATATTTGAAAGTATGTGAGGCTTTTGTAAAACACTTGCTCCCAAGTCTAATAATTAAATAGTTTCTGTGGGGTATAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.50% 33.40% 0.08% 0.00% NA
All Indica  2759 46.90% 53.00% 0.07% 0.00% NA
All Japonica  1512 96.00% 3.90% 0.13% 0.00% NA
Aus  269 89.60% 10.40% 0.00% 0.00% NA
Indica I  595 20.80% 79.20% 0.00% 0.00% NA
Indica II  465 30.80% 69.20% 0.00% 0.00% NA
Indica III  913 77.50% 22.30% 0.11% 0.00% NA
Indica Intermediate  786 40.60% 59.30% 0.13% 0.00% NA
Temperate Japonica  767 92.80% 6.90% 0.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 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
vg0500670256 C -> G LOC_Os05g02160.1 downstream_gene_variant ; 1993.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500670256 C -> G LOC_Os05g02150-LOC_Os05g02160 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500670256 NA 7.06E-06 mr1170 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
vg0500670256 NA 3.51E-07 mr1215 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
vg0500670256 NA 8.80E-06 mr1306 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
vg0500670256 NA 3.39E-14 mr1352 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
vg0500670256 NA 4.45E-08 mr1352 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
vg0500670256 NA 7.71E-12 mr1751 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
vg0500670256 NA 5.79E-06 mr1751 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