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Detailed information for vg0719735381:

Variant ID: vg0719735381 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19735381
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATCCTTCCGGCAAACCATACATACGTACGGGAGAAAGGTAGATCTAATTCATTGGTATAAAATAATGGGTCCACCAATTTAAGTGAAAATCAATGACA[G/T,A]
ATAAAGATCTAATCTAACAATGTAAAATAATGGGTCCACAATTTAAGTGAAAATCGACAGTGAAATTATATTGTGCCATATGGCGGCCTAGGAGCATTTG

Reverse complement sequence

CAAATGCTCCTAGGCCGCCATATGGCACAATATAATTTCACTGTCGATTTTCACTTAAATTGTGGACCCATTATTTTACATTGTTAGATTAGATCTTTAT[C/A,T]
TGTCATTGATTTTCACTTAAATTGGTGGACCCATTATTTTATACCAATGAATTAGATCTACCTTTCTCCCGTACGTATGTATGGTTTGCCGGAAGGATGA

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 94.50% 2.20% 2.92% 0.00% T: 0.34%
All Indica  2759 99.20% 0.20% 0.07% 0.00% T: 0.58%
All Japonica  1512 84.30% 6.70% 8.99% 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 99.10% 0.40% 0.43% 0.00% NA
Indica III  913 98.20% 0.00% 0.00% 0.00% T: 1.75%
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 75.60% 10.80% 13.56% 0.00% NA
Tropical Japonica  504 97.00% 0.80% 2.18% 0.00% NA
Japonica Intermediate  241 85.50% 5.80% 8.71% 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
vg0719735381 G -> A LOC_Os07g33040.1 upstream_gene_variant ; 1073.0bp to feature; MODIFIER silent_mutation Average:38.413; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0719735381 G -> A LOC_Os07g33030.1 downstream_gene_variant ; 2853.0bp to feature; MODIFIER silent_mutation Average:38.413; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0719735381 G -> A LOC_Os07g33030-LOC_Os07g33040 intergenic_region ; MODIFIER silent_mutation Average:38.413; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0719735381 G -> T LOC_Os07g33040.1 upstream_gene_variant ; 1073.0bp to feature; MODIFIER silent_mutation Average:38.413; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0719735381 G -> T LOC_Os07g33030.1 downstream_gene_variant ; 2853.0bp to feature; MODIFIER silent_mutation Average:38.413; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0719735381 G -> T LOC_Os07g33030-LOC_Os07g33040 intergenic_region ; MODIFIER silent_mutation Average:38.413; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719735381 2.33E-06 NA mr1707 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