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Detailed information for vg0528707182:

Variant ID: vg0528707182 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 28707182
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: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCCGCCCTCGGTCCAAAACCTGCTTGGCACCGGCCGTGCGCTGCGCGCGAGGAGGAGGCGACTCCGGCTCGGGGCAAGGTCGGACTCGGGAAGCGGAG[G/A]
AGACGAGGCCGTGCGCAGTCGCGTTGTGCATGCACGCCCACCACGTGCTCTCGCCAGCCGCGGGCGCGATGACAACGACCACCGCTGCCATCACCGTCGA

Reverse complement sequence

TCGACGGTGATGGCAGCGGTGGTCGTTGTCATCGCGCCCGCGGCTGGCGAGAGCACGTGGTGGGCGTGCATGCACAACGCGACTGCGCACGGCCTCGTCT[C/T]
CTCCGCTTCCCGAGTCCGACCTTGCCCCGAGCCGGAGTCGCCTCCTCCTCGCGCGCAGCGCACGGCCGGTGCCAAGCAGGTTTTGGACCGAGGGCGGACG

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 83.20% 12.90% 3.91% 0.00% NA
All Indica  2759 71.40% 21.90% 6.67% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 31.60% 44.90% 23.53% 0.00% NA
Indica II  465 86.20% 11.80% 1.94% 0.00% NA
Indica III  913 85.70% 13.40% 0.99% 0.00% NA
Indica Intermediate  786 76.30% 20.40% 3.31% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 94.40% 4.40% 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
vg0528707182 G -> A LOC_Os05g50080.1 downstream_gene_variant ; 2675.0bp to feature; MODIFIER silent_mutation Average:64.515; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 N N N N
vg0528707182 G -> A LOC_Os05g50100.1 downstream_gene_variant ; 3138.0bp to feature; MODIFIER silent_mutation Average:64.515; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 N N N N
vg0528707182 G -> A LOC_Os05g50090.1 intron_variant ; MODIFIER silent_mutation Average:64.515; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528707182 3.72E-07 2.18E-36 mr1026 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
vg0528707182 1.48E-06 5.29E-20 mr1026 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
vg0528707182 NA 2.54E-13 mr1118 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
vg0528707182 3.33E-06 1.47E-32 mr1161 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
vg0528707182 8.37E-06 1.43E-17 mr1161 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
vg0528707182 NA 3.67E-15 mr1495 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
vg0528707182 NA 8.33E-07 mr1496 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
vg0528707182 NA 1.03E-06 mr1870 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
vg0528707182 NA 4.69E-06 mr1027_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
vg0528707182 NA 1.38E-16 mr1118_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
vg0528707182 NA 5.70E-18 mr1118_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
vg0528707182 NA 1.81E-06 mr1123_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
vg0528707182 1.47E-07 5.11E-38 mr1161_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
vg0528707182 5.18E-07 7.19E-22 mr1161_2 Ind_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
vg0528707182 NA 1.74E-06 mr1242_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
vg0528707182 NA 1.87E-23 mr1495_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
vg0528707182 6.71E-06 1.66E-19 mr1495_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
vg0528707182 NA 2.54E-07 mr1496_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
vg0528707182 NA 3.94E-07 mr1531_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
vg0528707182 NA 1.33E-06 mr1870_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
vg0528707182 NA 2.86E-09 mr1936_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