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Detailed information for vg0431033243:

Variant ID: vg0431033243 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31033243
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTTTTGAGAATTACACAGTACAACGCAGACACTTACAATGTACGCACACTCACCCCTACGAACGCACGCATGTAAACTCTACCCCTATGAGCATATTC[G/A]
AAGACTGGGCCGGCAAATCCTAGAGATTGACGAAGTCACCACAGGCGTCTCACTGTCGACGGGTACGTCGCCTAGACTAGGTGCGAACTACTGTCCAGAG

Reverse complement sequence

CTCTGGACAGTAGTTCGCACCTAGTCTAGGCGACGTACCCGTCGACAGTGAGACGCCTGTGGTGACTTCGTCAATCTCTAGGATTTGCCGGCCCAGTCTT[C/T]
GAATATGCTCATAGGGGTAGAGTTTACATGCGTGCGTTCGTAGGGGTGAGTGTGCGTACATTGTAAGTGTCTGCGTTGTACTGTGTAATTCTCAAAAATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 2.80% 0.06% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 91.70% 8.10% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 83.80% 15.80% 0.39% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 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
vg0431033243 G -> A LOC_Os04g52240.1 upstream_gene_variant ; 1803.0bp to feature; MODIFIER silent_mutation Average:49.633; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0431033243 G -> A LOC_Os04g52230.1 downstream_gene_variant ; 1995.0bp to feature; MODIFIER silent_mutation Average:49.633; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0431033243 G -> A LOC_Os04g52230-LOC_Os04g52240 intergenic_region ; MODIFIER silent_mutation Average:49.633; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431033243 NA 3.94E-07 mr1062_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
vg0431033243 2.55E-06 2.55E-06 mr1445_2 Jap_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