Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0329146373:

Variant ID: vg0329146373 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 29146373
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAAGAGACCTGCTACAAAACGAGATCCCATTGCAACGGGATAGACATATCACAGGTACCATGTCCTAGATATCACGGGTACCGGGAAACAGGTATCGA[G/A]
TACCATGCAGCTGATACCACAACAAGTATCAGGTATCAGGTACTGTATCGTAGAAGGATATCCTGTTCCAACGGTATCATACCGTTGTCTAGGTTTTCTG

Reverse complement sequence

CAGAAAACCTAGACAACGGTATGATACCGTTGGAACAGGATATCCTTCTACGATACAGTACCTGATACCTGATACTTGTTGTGGTATCAGCTGCATGGTA[C/T]
TCGATACCTGTTTCCCGGTACCCGTGATATCTAGGACATGGTACCTGTGATATGTCTATCCCGTTGCAATGGGATCTCGTTTTGTAGCAGGTCTCTTAAT

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 97.30% 1.80% 0.83% 0.00% NA
All Indica  2759 99.50% 0.40% 0.18% 0.00% NA
All Japonica  1512 93.40% 4.40% 2.18% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 88.40% 8.10% 3.52% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 96.70% 2.10% 1.24% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0329146373 G -> A LOC_Os03g51000.1 upstream_gene_variant ; 823.0bp to feature; MODIFIER silent_mutation Average:69.152; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0329146373 G -> A LOC_Os03g51000.3 upstream_gene_variant ; 823.0bp to feature; MODIFIER silent_mutation Average:69.152; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0329146373 G -> A LOC_Os03g51000.2 upstream_gene_variant ; 821.0bp to feature; MODIFIER silent_mutation Average:69.152; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0329146373 G -> A LOC_Os03g51010.1 downstream_gene_variant ; 3747.0bp to feature; MODIFIER silent_mutation Average:69.152; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0329146373 G -> A LOC_Os03g51000-LOC_Os03g51010 intergenic_region ; MODIFIER silent_mutation Average:69.152; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0329146373 5.86E-07 5.86E-07 mr1024_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
vg0329146373 NA 1.90E-06 mr1565_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
vg0329146373 3.26E-07 3.26E-07 mr1915_2 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