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Detailed information for vg1202574324:

Variant ID: vg1202574324 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2574324
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTATAGATCGTCAGCCATCGCTCAAACGATTCGACACTCGAGGGTAAAATTTACTTAAAAAAATGTACACAAAGGGTAACATTACACGCATTTATATA[G/C]
TCAACTATATTTTGCAGTTTTAGTAAAACTTGGAGTAATCCAAACTGGAGCTAGTGGCCAATTCAGCCACGGCTGAGGATACTCCACATCGATCGCAGTG

Reverse complement sequence

CACTGCGATCGATGTGGAGTATCCTCAGCCGTGGCTGAATTGGCCACTAGCTCCAGTTTGGATTACTCCAAGTTTTACTAAAACTGCAAAATATAGTTGA[C/G]
TATATAAATGCGTGTAATGTTACCCTTTGTGTACATTTTTTTAAGTAAATTTTACCCTCGAGTGTCGAATCGTTTGAGCGATGGCTGACGATCTATAAAA

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 92.60% 7.40% 0.00% 0.00% NA
All Indica  2759 89.90% 10.10% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 75.10% 24.90% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 86.70% 13.30% 0.00% 0.00% NA
Indica Intermediate  786 84.40% 15.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 97.80% 2.20% 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
vg1202574324 G -> C LOC_Os12g05600.1 downstream_gene_variant ; 409.0bp to feature; MODIFIER silent_mutation Average:19.102; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg1202574324 G -> C LOC_Os12g05609.1 downstream_gene_variant ; 1.0bp to feature; MODIFIER silent_mutation Average:19.102; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg1202574324 G -> C LOC_Os12g05600-LOC_Os12g05609 intergenic_region ; MODIFIER silent_mutation Average:19.102; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202574324 1.84E-06 NA mr1013 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
vg1202574324 NA 9.42E-06 mr1125 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
vg1202574324 NA 6.54E-06 mr1533 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