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Detailed information for vg0704600543:

Variant ID: vg0704600543 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4600543
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGGATTGTTGAAAGTCCATTCCCTTTTATTTTTATGTTTGTGAACAAACTAAGATAGAATAGTAAAACCATCTAGATTAGTGGTATTATCATGCTGAA[C/A]
AGACTATATAACATCGAGAAATGACTAAAGATGATGTACATTAATAAAATACATGTTTTACTAATATCCAACACAATTCTCATATAGATGTAAGTCATTG

Reverse complement sequence

CAATGACTTACATCTATATGAGAATTGTGTTGGATATTAGTAAAACATGTATTTTATTAATGTACATCATCTTTAGTCATTTCTCGATGTTATATAGTCT[G/T]
TTCAGCATGATAATACCACTAATCTAGATGGTTTTACTATTCTATCTTAGTTTGTTCACAAACATAAAAATAAAAGGGAATGGACTTTCAACAATCCTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.80% 11.00% 0.15% 0.00% NA
All Indica  2759 95.30% 4.40% 0.25% 0.00% NA
All Japonica  1512 75.00% 25.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.10% 11.30% 0.67% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 95.70% 3.90% 0.38% 0.00% NA
Temperate Japonica  767 56.20% 43.80% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0704600543 C -> A LOC_Os07g08860.1 upstream_gene_variant ; 4936.0bp to feature; MODIFIER silent_mutation Average:61.701; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0704600543 C -> A LOC_Os07g08870.1 upstream_gene_variant ; 3004.0bp to feature; MODIFIER silent_mutation Average:61.701; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0704600543 C -> A LOC_Os07g08870-LOC_Os07g08880 intergenic_region ; MODIFIER silent_mutation Average:61.701; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704600543 1.25E-06 8.66E-09 mr1707 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
vg0704600543 NA 2.28E-06 mr1728 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
vg0704600543 NA 1.68E-07 mr1860 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
vg0704600543 2.54E-08 2.39E-09 mr1707_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