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Detailed information for vg1007541835:

Variant ID: vg1007541835 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7541835
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: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTTCTATAGTTAATCAACTATGTTACCTTAAATATACATGGTGTGTTCTAGATTCTGAAATGTTTAGCAAACTTAGGCAACATGTAGATTAACTATCA[C/A]
AATTTATGTCACTTTTTCATATCCAGCGAACTTATCTAACTTTTCTTTTCAGGTTACAAAAAATGCAGGAAAAATGTTTAGACTGTCGAAGCAAATCCAT

Reverse complement sequence

ATGGATTTGCTTCGACAGTCTAAACATTTTTCCTGCATTTTTTGTAACCTGAAAAGAAAAGTTAGATAAGTTCGCTGGATATGAAAAAGTGACATAAATT[G/T]
TGATAGTTAATCTACATGTTGCCTAAGTTTGCTAAACATTTCAGAATCTAGAACACACCATGTATATTTAAGGTAACATAGTTGATTAACTATAGAACAT

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 92.80% 5.80% 1.48% 0.00% NA
All Indica  2759 99.90% 0.10% 0.07% 0.00% NA
All Japonica  1512 78.10% 17.50% 4.37% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 60.00% 33.00% 7.04% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 90.50% 5.00% 4.56% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 5.60% 2.22% 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
vg1007541835 C -> A LOC_Os10g13870.1 upstream_gene_variant ; 2559.0bp to feature; MODIFIER silent_mutation Average:28.064; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg1007541835 C -> A LOC_Os10g13880.1 downstream_gene_variant ; 2100.0bp to feature; MODIFIER silent_mutation Average:28.064; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg1007541835 C -> A LOC_Os10g13870-LOC_Os10g13880 intergenic_region ; MODIFIER silent_mutation Average:28.064; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1007541835 6.45E-06 NA mr1768 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
vg1007541835 1.05E-14 7.13E-32 mr1768_2 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
vg1007541835 2.41E-07 2.53E-11 mr1768_2 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