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Detailed information for vg0321811925:

Variant ID: vg0321811925 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21811925
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAATAGTTTCCCGACTGACTGACGAATAAACTCCAAATAAAATTTTACTAAAACCCTAGACTAAGCTAATTTTAAAGATCCGATCCGAATGAACGACCAA[G/A]
ATTTTTCCCACAAACCAAAGAGGCAAAACACCAAATTTTTTCCGAAACAAATCCAAGTGCAAAGAGCATATGCAGATGAAAAGGGGATCAAAGGGCTCTT

Reverse complement sequence

AAGAGCCCTTTGATCCCCTTTTCATCTGCATATGCTCTTTGCACTTGGATTTGTTTCGGAAAAAATTTGGTGTTTTGCCTCTTTGGTTTGTGGGAAAAAT[C/T]
TTGGTCGTTCATTCGGATCGGATCTTTAAAATTAGCTTAGTCTAGGGTTTTAGTAAAATTTTATTTGGAGTTTATTCGTCAGTCAGTCGGGAAACTATTG

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 98.40% 1.50% 0.13% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.20% 4.40% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 86.10% 12.90% 0.99% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0321811925 G -> A LOC_Os03g39250.1 upstream_gene_variant ; 645.0bp to feature; MODIFIER silent_mutation Average:10.427; most accessible tissue: Callus, score: 35.451 N N N N
vg0321811925 G -> A LOC_Os03g39270.1 downstream_gene_variant ; 4211.0bp to feature; MODIFIER silent_mutation Average:10.427; most accessible tissue: Callus, score: 35.451 N N N N
vg0321811925 G -> A LOC_Os03g39250-LOC_Os03g39270 intergenic_region ; MODIFIER silent_mutation Average:10.427; most accessible tissue: Callus, score: 35.451 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321811925 NA 2.22E-07 mr1136 Jap_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
vg0321811925 NA 2.63E-07 mr1583 Jap_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
vg0321811925 1.62E-06 2.04E-08 mr1136_2 Jap_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
vg0321811925 NA 1.62E-07 mr1188_2 Jap_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