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Detailed information for vg0123987202:

Variant ID: vg0123987202 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23987202
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATTCGGATTCAAATATTTTTTATATAGAATATTTCTATACATAAAGTTTATGCATGCAAAGTTTACGATATAAAGTCTATGCACATGAATGAGAGTAGG[G/A]
GTGAAAATGGTAACAGAAATTCCCGGCCGTCCGGTGTTCATTTCCGACTTTCTACCGGCCAAGCCATACGGAAATGGTAATCGACCGATAAAATATGGAA

Reverse complement sequence

TTCCATATTTTATCGGTCGATTACCATTTCCGTATGGCTTGGCCGGTAGAAAGTCGGAAATGAACACCGGACGGCCGGGAATTTCTGTTACCATTTTCAC[C/T]
CCTACTCTCATTCATGTGCATAGACTTTATATCGTAAACTTTGCATGCATAAACTTTATGTATAGAAATATTCTATATAAAAAATATTTGAATCCGAATT

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 92.70% 7.20% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 77.60% 22.20% 0.13% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 71.60% 28.20% 0.26% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 61.80% 38.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0123987202 G -> A LOC_Os01g42294-LOC_Os01g42310 intergenic_region ; MODIFIER silent_mutation Average:27.725; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123987202 NA 2.05E-06 mr1070 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
vg0123987202 NA 4.56E-06 mr1097 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
vg0123987202 1.81E-06 1.81E-06 mr1128 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
vg0123987202 NA 9.62E-07 mr1154 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
vg0123987202 NA 1.20E-06 mr1092_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