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Detailed information for vg1003603685:

Variant ID: vg1003603685 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3603685
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGGCCACCAACAACCACTTGCACTTCGTGTGGAATATCTTCAACTTGCTTACGCAAGCCCTTCAATATTACCATAGCCCTCTCGTACGCATTATATAT[A/G]
TACTAGCAAAAATGCCCGTGCGTTGCAACGGGTGAAAAAATTCTAATGATAATATACGTTTTTCATGAATAATCATGTCAATGACAATGTTTGTATTTTA

Reverse complement sequence

TAAAATACAAACATTGTCATTGACATGATTATTCATGAAAAACGTATATTATCATTAGAATTTTTTCACCCGTTGCAACGCACGGGCATTTTTGCTAGTA[T/C]
ATATATAATGCGTACGAGAGGGCTATGGTAATATTGAAGGGCTTGCGTAAGCAAGTTGAAGATATTCCACACGAAGTGCAAGTGGTTGTTGGTGGCCCGA

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 75.40% 24.50% 0.08% 0.00% NA
All Indica  2759 66.70% 33.20% 0.11% 0.00% NA
All Japonica  1512 89.20% 10.80% 0.00% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 67.40% 32.40% 0.17% 0.00% NA
Indica II  465 68.00% 32.00% 0.00% 0.00% NA
Indica III  913 72.70% 27.10% 0.22% 0.00% NA
Indica Intermediate  786 58.40% 41.60% 0.00% 0.00% NA
Temperate Japonica  767 95.20% 4.80% 0.00% 0.00% NA
Tropical Japonica  504 79.20% 20.80% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 65.60% 34.40% 0.00% 0.00% NA
Intermediate  90 72.20% 26.70% 1.11% 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
vg1003603685 A -> G LOC_Os10g06910.1 downstream_gene_variant ; 3476.0bp to feature; MODIFIER silent_mutation Average:36.657; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 N N N N
vg1003603685 A -> G LOC_Os10g06920.1 downstream_gene_variant ; 1471.0bp to feature; MODIFIER silent_mutation Average:36.657; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 N N N N
vg1003603685 A -> G LOC_Os10g06920-LOC_Os10g06930 intergenic_region ; MODIFIER silent_mutation Average:36.657; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003603685 8.26E-09 1.03E-16 mr1709 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
vg1003603685 2.25E-07 1.18E-11 mr1709 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
vg1003603685 NA 1.67E-07 mr1547_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
vg1003603685 2.75E-12 6.34E-21 mr1709_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
vg1003603685 8.17E-11 1.63E-18 mr1709_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