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Detailed information for vg0321306372:

Variant ID: vg0321306372 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21306372
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCCGTCGTTTTGGTACTGTGTGCGGGACCACGCTTCCAGTGCACGGAACATGAACCGGATCAGGACTCGCACATACGAACGAAGCCTTAGAAACTAGTG[A/G]
TGTACTCTACTCTTTTCCAATGGTCTTTATCAGTACTCTGATCTAGACCACATATTTGAAAGTTTCTGGATTTCCGGTACCTCAAATTTTTAAAAGGTTT

Reverse complement sequence

AAACCTTTTAAAAATTTGAGGTACCGGAAATCCAGAAACTTTCAAATATGTGGTCTAGATCAGAGTACTGATAAAGACCATTGGAAAAGAGTAGAGTACA[T/C]
CACTAGTTTCTAAGGCTTCGTTCGTATGTGCGAGTCCTGATCCGGTTCATGTTCCGTGCACTGGAAGCGTGGTCCCGCACACAGTACCAAAACGACGGCT

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 63.90% 35.90% 0.15% 0.00% NA
All Indica  2759 97.30% 2.60% 0.14% 0.00% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 98.00% 1.80% 0.17% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 98.00% 1.90% 0.11% 0.00% NA
Indica Intermediate  786 96.30% 3.40% 0.25% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 4.40% 95.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 45.60% 51.10% 3.33% 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
vg0321306372 A -> G LOC_Os03g38370.1 upstream_gene_variant ; 3091.0bp to feature; MODIFIER silent_mutation Average:45.029; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 N N N N
vg0321306372 A -> G LOC_Os03g38375.1 upstream_gene_variant ; 243.0bp to feature; MODIFIER silent_mutation Average:45.029; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 N N N N
vg0321306372 A -> G LOC_Os03g38390.1 downstream_gene_variant ; 286.0bp to feature; MODIFIER silent_mutation Average:45.029; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 N N N N
vg0321306372 A -> G LOC_Os03g38375-LOC_Os03g38390 intergenic_region ; MODIFIER silent_mutation Average:45.029; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321306372 NA 1.83E-06 mr1334 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
vg0321306372 NA 2.31E-35 mr1670 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
vg0321306372 2.35E-12 5.27E-92 mr1718 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
vg0321306372 8.65E-10 1.65E-14 mr1718 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
vg0321306372 4.12E-18 1.09E-163 mr1750 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
vg0321306372 6.72E-14 3.44E-28 mr1750 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
vg0321306372 NA 5.66E-20 mr1838 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
vg0321306372 NA 2.04E-16 mr1842 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
vg0321306372 NA 1.04E-113 mr1987 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
vg0321306372 3.08E-07 3.08E-07 mr1987 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
vg0321306372 NA 4.01E-16 mr1342_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
vg0321306372 NA 1.38E-67 mr1594_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
vg0321306372 NA 6.88E-08 mr1645_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
vg0321306372 NA 1.36E-12 mr1713_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
vg0321306372 2.27E-18 2.13E-140 mr1718_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
vg0321306372 2.71E-13 2.22E-24 mr1718_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
vg0321306372 1.23E-22 1.72E-224 mr1750_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
vg0321306372 3.85E-17 3.17E-44 mr1750_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
vg0321306372 NA 6.05E-13 mr1770_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
vg0321306372 NA 1.18E-16 mr1842_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
vg0321306372 NA 1.53E-10 mr1893_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
vg0321306372 NA 5.88E-23 mr1933_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
vg0321306372 NA 1.99E-150 mr1987_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
vg0321306372 NA 1.89E-08 mr1987_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