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Detailed information for vg1003077652:

Variant ID: vg1003077652 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3077652
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, T: 0.11, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCCACAGCAGCCATCAGAGGGTTCAGGGTATCGCCGTGTCACACCATAAAGTTCTTCTCCCAAGCCTAAATCGTATTAATAAATGACCCCAATAAATT[G/A]
TTTGAGTAATGGCAAGAGAGAAACCCTAATTTAATAAATTCAATTAATAATCGGAATTAGCATGTGGAATTTTTCTTGGGTTCTACATGTCAAAATATGC

Reverse complement sequence

GCATATTTTGACATGTAGAACCCAAGAAAAATTCCACATGCTAATTCCGATTATTAATTGAATTTATTAAATTAGGGTTTCTCTCTTGCCATTACTCAAA[C/T]
AATTTATTGGGGTCATTTATTAATACGATTTAGGCTTGGGAGAAGAACTTTATGGTGTGACACGGCGATACCCTGAACCCTCTGATGGCTGCTGTGGCTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.70% 8.70% 0.08% 0.51% NA
All Indica  2759 84.20% 14.80% 0.14% 0.87% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.20% 17.60% 0.17% 0.00% NA
Indica II  465 86.90% 12.70% 0.22% 0.22% NA
Indica III  913 83.10% 14.60% 0.22% 2.08% NA
Indica Intermediate  786 85.50% 14.00% 0.00% 0.51% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1003077652 G -> A LOC_Os10g06050.1 downstream_gene_variant ; 1272.0bp to feature; MODIFIER silent_mutation Average:27.395; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg1003077652 G -> A LOC_Os10g06070.1 downstream_gene_variant ; 2440.0bp to feature; MODIFIER silent_mutation Average:27.395; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg1003077652 G -> A LOC_Os10g06050-LOC_Os10g06070 intergenic_region ; MODIFIER silent_mutation Average:27.395; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg1003077652 G -> DEL N N silent_mutation Average:27.395; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003077652 4.73E-06 2.05E-07 mr1538 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
vg1003077652 5.25E-10 1.44E-09 mr1547 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
vg1003077652 1.13E-08 2.22E-10 mr1547 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
vg1003077652 1.01E-12 1.60E-14 mr1709 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
vg1003077652 1.52E-10 1.03E-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
vg1003077652 NA 4.19E-06 mr1015_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
vg1003077652 NA 6.70E-09 mr1538_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
vg1003077652 1.07E-11 6.29E-13 mr1547_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
vg1003077652 3.27E-11 2.83E-14 mr1547_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
vg1003077652 1.16E-17 8.36E-15 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
vg1003077652 1.45E-12 1.81E-12 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
vg1003077652 NA 1.53E-06 mr1721_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