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Detailed information for vg0702789120:

Variant ID: vg0702789120 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2789120
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCTTTGGATGGCGAATATATCGATTGGAAAATAATTGAAAAATTTGAAGAAGCATCCCCCAAATTTAAAAAGAATTGAAAGAAGAAATACTTAAAGAAT[T/C]
AAAGAAATAAATGAATGATAAATTTGAAGAAATGAAAAAAGCATATGATGAAAAATTTGAAGTCTCCTTTTCTGATGTAGATACTATGGATTTAGGTGGT

Reverse complement sequence

ACCACCTAAATCCATAGTATCTACATCAGAAAAGGAGACTTCAAATTTTTCATCATATGCTTTTTTCATTTCTTCAAATTTATCATTCATTTATTTCTTT[A/G]
ATTCTTTAAGTATTTCTTCTTTCAATTCTTTTTAAATTTGGGGGATGCTTCTTCAAATTTTTCAATTATTTTCCAATCGATATATTCGCCATCCAAAGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 1.40% 1.06% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 92.60% 4.30% 3.11% 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 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 85.70% 8.30% 6.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 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
vg0702789120 T -> C LOC_Os07g05800.1 upstream_gene_variant ; 2330.0bp to feature; MODIFIER silent_mutation Average:16.339; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg0702789120 T -> C LOC_Os07g05810.1 upstream_gene_variant ; 4988.0bp to feature; MODIFIER silent_mutation Average:16.339; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg0702789120 T -> C LOC_Os07g05780.1 downstream_gene_variant ; 3613.0bp to feature; MODIFIER silent_mutation Average:16.339; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg0702789120 T -> C LOC_Os07g05790.1 downstream_gene_variant ; 697.0bp to feature; MODIFIER silent_mutation Average:16.339; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg0702789120 T -> C LOC_Os07g05790-LOC_Os07g05800 intergenic_region ; MODIFIER silent_mutation Average:16.339; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702789120 3.39E-06 3.39E-06 mr1464 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
vg0702789120 NA 7.72E-06 mr1648 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
vg0702789120 2.44E-06 NA mr1968 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