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Detailed information for vg0906442847:

Variant ID: vg0906442847 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6442847
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CTATATAGTACATTCAAAAAGAAAACCAGATTATTTCTTCATGCGATTGTTACAATGCTGGGAGACGGTGGATTATTTGAGATTGCTAGTTAAACTGCAT[T/A]
TTCCTCGTGATCTGAAGGAGGAAGAAAAGGTGGCTGCCATCGCCATGGCAGGGTGTAGAGGAATAACTTGAAGCACATTGGAGAAGCTCATGGATTCTAG

Reverse complement sequence

CTAGAATCCATGAGCTTCTCCAATGTGCTTCAAGTTATTCCTCTACACCCTGCCATGGCGATGGCAGCCACCTTTTCTTCCTCCTTCAGATCACGAGGAA[A/T]
ATGCAGTTTAACTAGCAATCTCAAATAATCCACCGTCTCCCAGCATTGTAACAATCGCATGAAGAAATAATCTGGTTTTCTTTTTGAATGTACTATATAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.70% 22.30% 0.04% 0.00% NA
All Indica  2759 68.40% 31.50% 0.07% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 58.40% 41.60% 0.00% 0.00% NA
Indica I  595 96.10% 3.90% 0.00% 0.00% NA
Indica II  465 45.60% 54.20% 0.22% 0.00% NA
Indica III  913 64.30% 35.70% 0.00% 0.00% NA
Indica Intermediate  786 65.80% 34.10% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 55.20% 44.80% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0906442847 T -> A LOC_Os09g11510.1 upstream_gene_variant ; 3922.0bp to feature; MODIFIER silent_mutation Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N
vg0906442847 T -> A LOC_Os09g11520.1 upstream_gene_variant ; 942.0bp to feature; MODIFIER silent_mutation Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N
vg0906442847 T -> A LOC_Os09g11550.1 upstream_gene_variant ; 3204.0bp to feature; MODIFIER silent_mutation Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N
vg0906442847 T -> A LOC_Os09g11540.1 downstream_gene_variant ; 2013.0bp to feature; MODIFIER silent_mutation Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N
vg0906442847 T -> A LOC_Os09g11530.1 intron_variant ; MODIFIER silent_mutation Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906442847 3.81E-06 NA mr1004_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
vg0906442847 5.58E-06 7.92E-06 mr1004_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