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Detailed information for vg0325679193:

Variant ID: vg0325679193 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 25679193
Reference Allele: TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGACAlternative Allele: T,CGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC
Primary Allele: TGGTGGCATAATAGGCCAGC CGTGTAGGCGGAGACSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCCCAACAACAGTGGCATAATAGGCCAGCCGTGTAGGCGGAGACACCAGTCGGCGGCAGCGAAAGCGAGACAACGGTGAAGTCGTAGACGCCCAACAA[TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC/T,CGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC]
ACCAGTCGGCAGCGGCGAAGATAAGCCGGTGATGATGATGCCCACCAATATTGACATGGTAGACCAGCCCGTTTTGTATCTTAGATTGAAGGTTGTCTGT

Reverse complement sequence

ACAGACAACCTTCAATCTAAGATACAAAACGGGCTGGTCTACCATGTCAATATTGGTGGGCATCATCATCACCGGCTTATCTTCGCCGCTGCCGACTGGT[GTCTCCGCCTACACGGCTGGCCTATTATGCCACCA/A,GTCTCCGCCTACACGGCTGGCCTATTATGCCACCG]
TTGTTGGGCGTCTACGACTTCACCGTTGTCTCGCTTTCGCTGCCGCCGACTGGTGTCTCCGCCTACACGGCTGGCCTATTATGCCACTGTTGTTGGGCGT

Allele Frequencies:

Populations Population SizeFrequency of TGGTGGCATAATAGGCCAGC CGTGTAGGCGGAGAC(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.20% 9.00% 1.23% 0.53% CGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC: 0.02%
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 76.20% 21.40% 0.79% 1.65% NA
Aus  269 75.50% 24.20% 0.37% 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 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 82.70% 16.80% 0.26% 0.26% NA
Tropical Japonica  504 75.00% 19.00% 1.59% 4.37% NA
Japonica Intermediate  241 58.10% 40.70% 0.83% 0.41% NA
VI/Aromatic  96 43.80% 10.40% 44.79% 0.00% CGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC: 1.04%
Intermediate  90 87.80% 10.00% 2.22% 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
vg0325679193 TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC -> T LOC_Os03g45500.1 downstream_gene_variant ; 500.0bp to feature; MODIFIER silent_mutation Average:70.038; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 N N N N
vg0325679193 TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC -> T LOC_Os03g45510.1 downstream_gene_variant ; 2733.0bp to feature; MODIFIER silent_mutation Average:70.038; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 N N N N
vg0325679193 TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC -> T LOC_Os03g45500-LOC_Os03g45510 intergenic_region ; MODIFIER silent_mutation Average:70.038; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 N N N N
vg0325679193 TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC -> CGGTGGCATAATAGGCCAGCCGTGTAGGCG GAGAC LOC_Os03g45500.1 downstream_gene_variant ; 499.0bp to feature; MODIFIER silent_mutation Average:70.038; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 N N N N
vg0325679193 TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC -> CGGTGGCATAATAGGCCAGCCGTGTAGGCG GAGAC LOC_Os03g45510.1 downstream_gene_variant ; 2734.0bp to feature; MODIFIER silent_mutation Average:70.038; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 N N N N
vg0325679193 TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC -> CGGTGGCATAATAGGCCAGCCGTGTAGGCG GAGAC LOC_Os03g45500-LOC_Os03g45510 intergenic_region ; MODIFIER silent_mutation Average:70.038; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 N N N N
vg0325679193 TGGTGGCATAATAGGCCAGCCGTGTAGGCGGAGAC -> DEL N N silent_mutation Average:70.038; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0325679193 1.47E-06 NA mr1246 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