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Detailed information for vg0323735156:

Variant ID: vg0323735156 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23735156
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGATTTTAGGGGAAATGTAGGCTCTTCTGTGTCCCTTTCGGACTTGTTCAAGAATTCCCTTTTGAGAAGAAATGCCAAAGGCCCTGCATGCTTTCATA[G/A]
AAAGCAGAAGACTTGTTCAATAATTCTCTCCTTTTAACTCTATACACTTTCTTCGATTAAGCTTTTTCTTATTCTCAGACTCGTTCTTTCTGATTGGTGA

Reverse complement sequence

TCACCAATCAGAAAGAACGAGTCTGAGAATAAGAAAAAGCTTAATCGAAGAAAGTGTATAGAGTTAAAAGGAGAGAATTATTGAACAAGTCTTCTGCTTT[C/T]
TATGAAAGCATGCAGGGCCTTTGGCATTTCTTCTCAAAAGGGAATTCTTGAACAAGTCCGAAAGGGACACAGAAGAGCCTACATTTCCCCTAAAATCAAC

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 95.20% 4.80% 0.02% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 29.00% 70.60% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 96.40% 3.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0323735156 G -> A LOC_Os03g42650.1 upstream_gene_variant ; 3729.0bp to feature; MODIFIER silent_mutation Average:65.482; most accessible tissue: Minghui63 root, score: 82.967 N N N N
vg0323735156 G -> A LOC_Os03g42650.2 upstream_gene_variant ; 3729.0bp to feature; MODIFIER silent_mutation Average:65.482; most accessible tissue: Minghui63 root, score: 82.967 N N N N
vg0323735156 G -> A LOC_Os03g42630.1 intron_variant ; MODIFIER silent_mutation Average:65.482; most accessible tissue: Minghui63 root, score: 82.967 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323735156 NA 5.75E-06 mr1006 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
vg0323735156 NA 5.85E-06 mr1052 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
vg0323735156 NA 2.53E-14 mr1166 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
vg0323735156 NA 1.18E-06 mr1320 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
vg0323735156 NA 9.17E-20 mr1515 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
vg0323735156 NA 6.90E-06 mr1808 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
vg0323735156 NA 3.96E-06 mr1344_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