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Detailed information for vg0214744055:

Variant ID: vg0214744055 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 14744055
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTAAACTAAACTTGAGAGAAATGAGAGAGCTATTGCTTGAGGTGTGTGAGTGAAGTGAGGAGAGGAGCTCCTTAAATAGGCTGCCAATGACGGTTGTG[G/A]
TAGTTAGAATGGTCGGAATTGCCCTCCAACTGTCATTGGGGAGTGATCCATACCGTCCAGCCAAAACCTGGATCCAACGGCGCCAGGGGAGGTTCAGCCG

Reverse complement sequence

CGGCTGAACCTCCCCTGGCGCCGTTGGATCCAGGTTTTGGCTGGACGGTATGGATCACTCCCCAATGACAGTTGGAGGGCAATTCCGACCATTCTAACTA[C/T]
CACAACCGTCATTGGCAGCCTATTTAAGGAGCTCCTCTCCTCACTTCACTCACACACCTCAAGCAATAGCTCTCTCATTTCTCTCAAGTTTAGTTTAGTA

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 95.60% 3.40% 0.99% 0.00% NA
All Indica  2759 92.50% 5.80% 1.70% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 79.30% 14.50% 6.22% 0.00% NA
Indica II  465 95.90% 3.40% 0.65% 0.00% NA
Indica III  913 98.80% 1.10% 0.11% 0.00% NA
Indica Intermediate  786 93.10% 6.10% 0.76% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0214744055 G -> A LOC_Os02g25290.1 upstream_gene_variant ; 2271.0bp to feature; MODIFIER silent_mutation Average:39.032; most accessible tissue: Minghui63 young leaf, score: 55.178 N N N N
vg0214744055 G -> A LOC_Os02g25280-LOC_Os02g25290 intergenic_region ; MODIFIER silent_mutation Average:39.032; most accessible tissue: Minghui63 young leaf, score: 55.178 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0214744055 NA 1.59E-06 mr1257_2 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
vg0214744055 4.20E-06 1.55E-07 mr1379_2 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