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Detailed information for vg0427734139:

Variant ID: vg0427734139 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27734139
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTCTATAGTAAAAATGCACATTGCACACGAGCCGATGTCCGATTTTAAAAGAAAACAAAAATTTCAGGTTCATCACAATCACATGTTAGCTAATGTA[A/G]
TACTAAAAATTTTCATGTCAAAGTTATCTCTAACGTGTTTTACCTAACAACCTTGTGATGCTTCTCCTGCAGAATGAGACTCTTGATGTCATTATCAAAA

Reverse complement sequence

TTTTGATAATGACATCAAGAGTCTCATTCTGCAGGAGAAGCATCACAAGGTTGTTAGGTAAAACACGTTAGAGATAACTTTGACATGAAAATTTTTAGTA[T/C]
TACATTAGCTAACATGTGATTGTGATGAACCTGAAATTTTTGTTTTCTTTTAAAATCGGACATCGGCTCGTGTGCAATGTGCATTTTTACTATAGAAAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.70% 33.70% 0.23% 0.38% NA
All Indica  2759 42.00% 57.00% 0.36% 0.62% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 19.80% 79.50% 0.34% 0.34% NA
Indica II  465 78.70% 21.10% 0.22% 0.00% NA
Indica III  913 32.50% 66.70% 0.33% 0.44% NA
Indica Intermediate  786 48.00% 50.10% 0.51% 1.40% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 77.80% 21.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0427734139 A -> DEL N N silent_mutation Average:52.795; most accessible tissue: Zhenshan97 root, score: 75.275 N N N N
vg0427734139 A -> G LOC_Os04g46780.2 3_prime_UTR_variant ; 327.0bp to feature; MODIFIER silent_mutation Average:52.795; most accessible tissue: Zhenshan97 root, score: 75.275 N N N N
vg0427734139 A -> G LOC_Os04g46800.1 upstream_gene_variant ; 4085.0bp to feature; MODIFIER silent_mutation Average:52.795; most accessible tissue: Zhenshan97 root, score: 75.275 N N N N
vg0427734139 A -> G LOC_Os04g46770.1 downstream_gene_variant ; 3086.0bp to feature; MODIFIER silent_mutation Average:52.795; most accessible tissue: Zhenshan97 root, score: 75.275 N N N N
vg0427734139 A -> G LOC_Os04g46790.1 downstream_gene_variant ; 2342.0bp to feature; MODIFIER silent_mutation Average:52.795; most accessible tissue: Zhenshan97 root, score: 75.275 N N N N
vg0427734139 A -> G LOC_Os04g46780.1 intron_variant ; MODIFIER silent_mutation Average:52.795; most accessible tissue: Zhenshan97 root, score: 75.275 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0427734139 NA 7.10E-08 mr1174 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
vg0427734139 NA 4.39E-07 mr1731 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
vg0427734139 NA 3.17E-09 mr1174_2 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
vg0427734139 NA 3.21E-08 mr1347_2 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
vg0427734139 NA 3.52E-06 mr1355_2 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