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Detailed information for vg0332522340:

Variant ID: vg0332522340 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 32522340
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCACGGCATTCAATGCCAGCTGACGTGGCGCTGAGGTATCTAAGTTCAACGCCACATGATTTGGCGTTGAGCAAAAAGGATCAGATTTGAAATAAGTTTT[G/A]
GCAGCGGTTCATTTGTAAAAATAGTTTTTGCAAAGGGTCAAACTGTCAAAATTTGTGAAGAAAAACAACCATAAGTTTAGAGTGCACCACAAGAGAATAA

Reverse complement sequence

TTATTCTCTTGTGGTGCACTCTAAACTTATGGTTGTTTTTCTTCACAAATTTTGACAGTTTGACCCTTTGCAAAAACTATTTTTACAAATGAACCGCTGC[C/T]
AAAACTTATTTCAAATCTGATCCTTTTTGCTCAACGCCAAATCATGTGGCGTTGAACTTAGATACCTCAGCGCCACGTCAGCTGGCATTGAATGCCGTGC

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 92.10% 6.90% 0.97% 0.00% NA
All Indica  2759 99.70% 0.10% 0.14% 0.00% NA
All Japonica  1512 77.10% 20.30% 2.58% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 92.80% 4.00% 3.13% 0.00% NA
Tropical Japonica  504 43.80% 53.60% 2.58% 0.00% NA
Japonica Intermediate  241 96.70% 2.50% 0.83% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 83.30% 13.30% 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
vg0332522340 G -> A LOC_Os03g57050.1 upstream_gene_variant ; 1289.0bp to feature; MODIFIER silent_mutation Average:46.504; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0332522340 G -> A LOC_Os03g57060.1 downstream_gene_variant ; 3844.0bp to feature; MODIFIER silent_mutation Average:46.504; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0332522340 G -> A LOC_Os03g57040-LOC_Os03g57050 intergenic_region ; MODIFIER silent_mutation Average:46.504; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0332522340 NA 4.48E-07 mr1807 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
vg0332522340 NA 5.21E-06 mr1942 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
vg0332522340 NA 1.99E-07 mr1551_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
vg0332522340 NA 9.97E-13 mr1905_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
vg0332522340 NA 2.31E-07 mr1905_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