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Detailed information for vg0200811680:

Variant ID: vg0200811680 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 811680
Reference Allele: GAlternative Allele: A,C
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCATTTCACCGCTTCACCGGAAATTCCCTCTGCCCCTACCGTACTCCAGCTTGGTAGTTTCCACCGCCTGTCCAGGGTTGAGCCCTGGGATTTGACGGC[G/A,C]
GTCTTGAAAAGCCACCTACAGACGCTTTACGCCTAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCACGGCTGCTGGCATAGAGTTAGCCGATGC

Reverse complement sequence

GCATCGGCTAACTCTATGCCAGCAGCCGTGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTAGGCGTAAAGCGTCTGTAGGTGGCTTTTCAAGAC[C/T,G]
GCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGAAGCGGTGAAATGCA

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 95.10% 4.70% 0.13% 0.00% C: 0.06%
All Indica  2759 92.00% 7.80% 0.22% 0.00% NA
All Japonica  1512 99.60% 0.30% 0.00% 0.00% C: 0.13%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.10% 6.60% 0.34% 0.00% NA
Indica II  465 79.80% 19.40% 0.86% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 88.90% 11.10% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.20% 0.00% 0.00% C: 0.40%
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 0.00% 0.00% C: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0200811680 G -> A LOC_Os02g02380-LOC_Os02g02390 intergenic_region ; MODIFIER silent_mutation Average:31.521; most accessible tissue: Callus, score: 56.111 N N N N
vg0200811680 G -> C LOC_Os02g02380-LOC_Os02g02390 intergenic_region ; MODIFIER silent_mutation Average:31.521; most accessible tissue: Callus, score: 56.111 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200811680 2.01E-06 2.01E-06 mr1259 Ind_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
vg0200811680 3.23E-06 3.23E-06 mr1299 Ind_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
vg0200811680 2.33E-06 2.33E-06 mr1756 Ind_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