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Detailed information for vg0907825771:

Variant ID: vg0907825771 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7825771
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.37, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGATTTTGTGAAGTGAGCTGTTTTGGTTGACCCTGGCGGTCAGACCGGCTGAGTGTCGCCGGTTAGACCGCGGGTGTTGCGGCGGTCAGACCGGCCGG[C/T]
CCGACGGTCTGACCGGCATGATCCTGATCGATGTCGGTTTCGGGTTGATTTGTTGGATTTGGCTTCTAGATGGTTTCTATGCGTATGGATACTATTGTTA

Reverse complement sequence

TAACAATAGTATCCATACGCATAGAAACCATCTAGAAGCCAAATCCAACAAATCAACCCGAAACCGACATCGATCAGGATCATGCCGGTCAGACCGTCGG[G/A]
CCGGCCGGTCTGACCGCCGCAACACCCGCGGTCTAACCGGCGACACTCAGCCGGTCTGACCGCCAGGGTCAACCAAAACAGCTCACTTCACAAAATCAAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.00% 27.00% 0.04% 0.00% NA
All Indica  2759 89.10% 10.90% 0.07% 0.00% NA
All Japonica  1512 43.30% 56.70% 0.00% 0.00% NA
Aus  269 66.20% 33.80% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 83.40% 16.60% 0.00% 0.00% NA
Indica III  913 89.90% 10.10% 0.00% 0.00% NA
Indica Intermediate  786 87.00% 12.70% 0.25% 0.00% NA
Temperate Japonica  767 27.00% 73.00% 0.00% 0.00% NA
Tropical Japonica  504 75.40% 24.60% 0.00% 0.00% NA
Japonica Intermediate  241 28.20% 71.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0907825771 C -> T LOC_Os09g13510.1 downstream_gene_variant ; 1288.0bp to feature; MODIFIER silent_mutation Average:42.374; most accessible tissue: Minghui63 young leaf, score: 58.21 N N N N
vg0907825771 C -> T LOC_Os09g13510-LOC_Os09g13520 intergenic_region ; MODIFIER silent_mutation Average:42.374; most accessible tissue: Minghui63 young leaf, score: 58.21 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907825771 1.31E-06 7.34E-09 mr1002 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
vg0907825771 NA 4.39E-12 mr1002 Jap_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
vg0907825771 NA 6.43E-09 mr1002_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
vg0907825771 NA 1.40E-10 mr1002_2 Jap_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
vg0907825771 NA 3.97E-06 mr1330_2 Jap_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
vg0907825771 NA 3.23E-10 mr1805_2 Jap_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