Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0517323033:

Variant ID: vg0517323033 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17323033
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGTGTCATGCGACGTGCTCTTCATAATATTTTATATAGTCACCGATGAATTTCGATCTATTAGGTCAGGAATTAACTCTGTTTGCAACTTTAGACAGT[G/C]
TTAGGAATGAAACTATATAATGTCTTTGACAATTTTGGAACATATTGACTGATATGAAAATTTTGGTACAAATGTGCGATGACACTCCAATTAAGAATAT

Reverse complement sequence

ATATTCTTAATTGGAGTGTCATCGCACATTTGTACCAAAATTTTCATATCAGTCAATATGTTCCAAAATTGTCAAAGACATTATATAGTTTCATTCCTAA[C/G]
ACTGTCTAAAGTTGCAAACAGAGTTAATTCCTGACCTAATAGATCGAAATTCATCGGTGACTATATAAAATATTATGAAGAGCACGTCGCATGACACAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.90% 2.20% 0.87% 0.00% NA
All Indica  2759 94.70% 3.80% 1.45% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.20% 10.80% 6.05% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 97.80% 2.10% 0.11% 0.00% NA
Indica Intermediate  786 96.90% 2.80% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0517323033 G -> C LOC_Os05g29930.1 upstream_gene_variant ; 3256.0bp to feature; MODIFIER silent_mutation Average:45.613; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0517323033 G -> C LOC_Os05g29940.1 upstream_gene_variant ; 1901.0bp to feature; MODIFIER silent_mutation Average:45.613; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0517323033 G -> C LOC_Os05g29950.1 upstream_gene_variant ; 2209.0bp to feature; MODIFIER silent_mutation Average:45.613; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0517323033 G -> C LOC_Os05g29940-LOC_Os05g29950 intergenic_region ; MODIFIER silent_mutation Average:45.613; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517323033 1.80E-06 1.80E-06 mr1276_2 Ind_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
vg0517323033 NA 3.94E-06 mr1349_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