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Detailed information for vg0723875740:

Variant ID: vg0723875740 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23875740
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCTGGACACCCGTGACATTATTTTATAATATCCAAAGGAAATGGAGAGAGAAACAAAAACAAAAGTATGATTGTGCCCCTTGCCTACCAAGTCCGGCTC[G/A]
CATACACCTCCGACACTGCAACTGCACCCGTTGCCGGTGAGGTGACTGTCTAGAGGGGGGAGGGGGTTTCGAGATATGGTATTTTGTAGATTTTTATGGT

Reverse complement sequence

ACCATAAAAATCTACAAAATACCATATCTCGAAACCCCCTCCCCCCTCTAGACAGTCACCTCACCGGCAACGGGTGCAGTTGCAGTGTCGGAGGTGTATG[C/T]
GAGCCGGACTTGGTAGGCAAGGGGCACAATCATACTTTTGTTTTTGTTTCTCTCTCCATTTCCTTTGGATATTATAAAATAATGTCACGGGTGTCCAGCA

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 94.60% 4.50% 0.97% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 83.90% 13.20% 2.91% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.25% 0.00% NA
Temperate Japonica  767 91.80% 5.10% 3.13% 0.00% NA
Tropical Japonica  504 72.00% 24.80% 3.17% 0.00% NA
Japonica Intermediate  241 83.40% 14.90% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0723875740 G -> A LOC_Os07g39820.1 downstream_gene_variant ; 4595.0bp to feature; MODIFIER silent_mutation Average:53.918; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0723875740 G -> A LOC_Os07g39820-LOC_Os07g39830 intergenic_region ; MODIFIER silent_mutation Average:53.918; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723875740 NA 2.86E-06 mr1170 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
vg0723875740 5.58E-06 NA mr1264 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
vg0723875740 3.28E-06 3.28E-06 mr1264 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
vg0723875740 NA 1.41E-06 mr1729 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
vg0723875740 NA 8.80E-06 mr1882 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
vg0723875740 NA 4.52E-06 mr1715_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