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Detailed information for vg0716058721:

Variant ID: vg0716058721 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16058721
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCACTGAAGCCGTTTCCTGTAGTAGTAAATCCATGGCATATGACCATATGAACTATAATCGTAAAGGTATAATTAGTGGATTGGTCAATATTTGAATGCC[G/A]
TTATCTGTGTCAGATTTGGTTTTATCTCTATAGTCAATAAATAAATTTGTAGTAAGAAAATATCCTATTAAAACCCATTATAAATATAGTCCATTGATTT

Reverse complement sequence

AAATCAATGGACTATATTTATAATGGGTTTTAATAGGATATTTTCTTACTACAAATTTATTTATTGACTATAGAGATAAAACCAAATCTGACACAGATAA[C/T]
GGCATTCAAATATTGACCAATCCACTAATTATACCTTTACGATTATAGTTCATATGGTCATATGCCATGGATTTACTACTACAGGAAACGGCTTCAGTGC

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 86.40% 13.10% 0.49% 0.00% NA
All Indica  2759 99.00% 0.90% 0.04% 0.00% NA
All Japonica  1512 61.70% 36.90% 1.39% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.20% 0.13% 0.00% NA
Temperate Japonica  767 82.50% 16.20% 1.30% 0.00% NA
Tropical Japonica  504 22.40% 76.20% 1.39% 0.00% NA
Japonica Intermediate  241 77.60% 20.70% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg0716058721 G -> A LOC_Os07g27490-LOC_Os07g27500 intergenic_region ; MODIFIER silent_mutation Average:40.421; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716058721 NA 1.57E-06 mr1321 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
vg0716058721 NA 2.31E-07 mr1554 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
vg0716058721 NA 6.64E-08 mr1648 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
vg0716058721 NA 5.08E-06 mr1697 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
vg0716058721 1.80E-07 NA mr1844 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
vg0716058721 7.43E-08 NA mr1844 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
vg0716058721 NA 5.43E-13 mr1900 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
vg0716058721 NA 1.23E-10 mr1905 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
vg0716058721 NA 3.21E-08 mr1310_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
vg0716058721 NA 1.19E-07 mr1696_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