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Detailed information for vg0307269169:

Variant ID: vg0307269169 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7269169
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGACCGGTGTTGATCTTCTGGTTGGACCGCCCTGGAATCCCTGTCGCGCCTGTTGTCGCCGCCGGTCTGACCGCAGGTCACCCGCCGGTCTGACCGCC[G/A]
TAATGCCGCCGGTCTGACCACCGGTGTGTCGCCGATTAGACCGCAAAAACCCAGTGAAACACAAATCGAAGAACTCTAAAAGTGGATGACGACTTTATTG

Reverse complement sequence

CAATAAAGTCGTCATCCACTTTTAGAGTTCTTCGATTTGTGTTTCACTGGGTTTTTGCGGTCTAATCGGCGACACACCGGTGGTCAGACCGGCGGCATTA[C/T]
GGCGGTCAGACCGGCGGGTGACCTGCGGTCAGACCGGCGGCGACAACAGGCGCGACAGGGATTCCAGGGCGGTCCAACCAGAAGATCAACACCGGTCAGA

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 61.00% 34.00% 5.04% 0.04% NA
All Indica  2759 94.20% 3.30% 2.50% 0.00% NA
All Japonica  1512 4.80% 95.00% 0.20% 0.00% NA
Aus  269 29.00% 11.90% 58.36% 0.74% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 90.30% 5.90% 3.83% 0.00% NA
Indica Intermediate  786 93.10% 2.70% 4.20% 0.00% NA
Temperate Japonica  767 2.00% 97.80% 0.26% 0.00% NA
Tropical Japonica  504 10.30% 89.50% 0.20% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 9.40% 5.21% 0.00% NA
Intermediate  90 54.40% 41.10% 4.44% 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
vg0307269169 G -> A LOC_Os03g13430.1 downstream_gene_variant ; 1632.0bp to feature; MODIFIER silent_mutation Average:31.118; most accessible tissue: Zhenshan97 root, score: 49.075 N N N N
vg0307269169 G -> A LOC_Os03g13430-LOC_Os03g13450 intergenic_region ; MODIFIER silent_mutation Average:31.118; most accessible tissue: Zhenshan97 root, score: 49.075 N N N N
vg0307269169 G -> DEL N N silent_mutation Average:31.118; most accessible tissue: Zhenshan97 root, score: 49.075 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307269169 NA 1.45E-07 mr1666 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
vg0307269169 NA 2.58E-06 mr1761 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
vg0307269169 NA 1.55E-11 mr1819 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
vg0307269169 NA 8.81E-10 mr1172_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
vg0307269169 NA 2.60E-23 mr1253_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
vg0307269169 NA 7.45E-13 mr1666_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
vg0307269169 NA 9.98E-32 mr1913_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
vg0307269169 2.64E-06 NA mr1928_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