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Detailed information for vg0419327742:

Variant ID: vg0419327742 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19327742
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTAAAAAATCTCAAAAAGTAGAGGGGAAAAGTGGGGAAATTATTGTCGAAATGTGTAGCTAGCCAGTTAAATTAAGAACACTGGCTAGTGGCTACTGT[G/A]
TATCACTCTGCTTGTTTGGCACGTGCGAACATAGCATACATTAACACAAGTTTAAACTACGTGCGTACATCAGCTATATTATATAGCCATATCACTTATC

Reverse complement sequence

GATAAGTGATATGGCTATATAATATAGCTGATGTACGCACGTAGTTTAAACTTGTGTTAATGTATGCTATGTTCGCACGTGCCAAACAAGCAGAGTGATA[C/T]
ACAGTAGCCACTAGCCAGTGTTCTTAATTTAACTGGCTAGCTACACATTTCGACAATAATTTCCCCACTTTTCCCCTCTACTTTTTGAGATTTTTTACAA

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 96.70% 2.80% 0.49% 0.00% NA
All Indica  2759 98.90% 0.90% 0.25% 0.00% NA
All Japonica  1512 92.20% 6.80% 0.99% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.00% 0.67% 0.00% NA
Indica II  465 96.80% 2.80% 0.43% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.30% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 83.50% 14.50% 1.98% 0.00% NA
Japonica Intermediate  241 86.30% 12.40% 1.24% 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
vg0419327742 G -> A LOC_Os04g32260.1 upstream_gene_variant ; 1345.0bp to feature; MODIFIER silent_mutation Average:37.462; most accessible tissue: Callus, score: 77.936 N N N N
vg0419327742 G -> A LOC_Os04g32250.1 downstream_gene_variant ; 591.0bp to feature; MODIFIER silent_mutation Average:37.462; most accessible tissue: Callus, score: 77.936 N N N N
vg0419327742 G -> A LOC_Os04g32250-LOC_Os04g32260 intergenic_region ; MODIFIER silent_mutation Average:37.462; most accessible tissue: Callus, score: 77.936 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419327742 NA 6.53E-06 mr1076 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
vg0419327742 NA 4.23E-06 mr1082 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
vg0419327742 3.23E-09 1.28E-11 mr1227 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
vg0419327742 NA 1.61E-06 mr1304 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
vg0419327742 NA 1.16E-06 mr1414 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
vg0419327742 NA 7.32E-07 mr1819 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
vg0419327742 NA 4.37E-08 mr1852 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