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Detailed information for vg0601373352:

Variant ID: vg0601373352 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1373352
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCTCATAAGTTTCGTGTGTATGTCCATCCTTTTTTCTTGAAAAGCTGATTTACTTAATAGCCAAATTTCACTGGAGACAAGTATCATGGTTCTTAACC[A/G]
CATTATTTTAATATTGTAGACAGTGGAGTGGCGAATCTAAGAAAAAAAAATACCTTCCATGGAAGAGGAGAGCATGAACAATTGTTGCAGCAAGGGTTGC

Reverse complement sequence

GCAACCCTTGCTGCAACAATTGTTCATGCTCTCCTCTTCCATGGAAGGTATTTTTTTTTCTTAGATTCGCCACTCCACTGTCTACAATATTAAAATAATG[T/C]
GGTTAAGAACCATGATACTTGTCTCCAGTGAAATTTGGCTATTAAGTAAATCAGCTTTTCAAGAAAAAAGGATGGACATACACACGAAACTTATGAGGAG

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 68.40% 31.50% 0.06% 0.00% NA
All Indica  2759 67.90% 32.00% 0.11% 0.00% NA
All Japonica  1512 72.80% 27.20% 0.00% 0.00% NA
Aus  269 63.20% 36.80% 0.00% 0.00% NA
Indica I  595 91.80% 8.10% 0.17% 0.00% NA
Indica II  465 78.10% 21.90% 0.00% 0.00% NA
Indica III  913 48.20% 51.80% 0.00% 0.00% NA
Indica Intermediate  786 66.50% 33.20% 0.25% 0.00% NA
Temperate Japonica  767 80.70% 19.30% 0.00% 0.00% NA
Tropical Japonica  504 60.90% 39.10% 0.00% 0.00% NA
Japonica Intermediate  241 72.60% 27.40% 0.00% 0.00% NA
VI/Aromatic  96 38.50% 61.50% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg0601373352 A -> G LOC_Os06g03540.1 upstream_gene_variant ; 4344.0bp to feature; MODIFIER silent_mutation Average:60.542; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0601373352 A -> G LOC_Os06g03570.2 upstream_gene_variant ; 4064.0bp to feature; MODIFIER silent_mutation Average:60.542; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0601373352 A -> G LOC_Os06g03570.1 upstream_gene_variant ; 4064.0bp to feature; MODIFIER silent_mutation Average:60.542; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0601373352 A -> G LOC_Os06g03550.1 downstream_gene_variant ; 2489.0bp to feature; MODIFIER silent_mutation Average:60.542; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0601373352 A -> G LOC_Os06g03560.1 intron_variant ; MODIFIER silent_mutation Average:60.542; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601373352 NA 7.66E-06 mr1236 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
vg0601373352 NA 5.03E-06 mr1414 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
vg0601373352 1.81E-06 NA mr1995 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