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Detailed information for vg0621702300:

Variant ID: vg0621702300 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21702300
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAAATGAACAAAATCATCCCATTCAACTGAAAATATTAGTTAGGGAAAATATTTACTTGAGGCATTTAAGTGCTTATTGGTTTTTTAACCATTTGTAG[A/G]
AACTGGGATCCAGGTTCTCACCTGTCAATATCAATTCAGCACCCAAAAACCTCAGTAGCATCTGCTTGTCAAGCGAATATTTAGCAGGCATGACAGCAAT

Reverse complement sequence

ATTGCTGTCATGCCTGCTAAATATTCGCTTGACAAGCAGATGCTACTGAGGTTTTTGGGTGCTGAATTGATATTGACAGGTGAGAACCTGGATCCCAGTT[T/C]
CTACAAATGGTTAAAAAACCAATAAGCACTTAAATGCCTCAAGTAAATATTTTCCCTAACTAATATTTTCAGTTGAATGGGATGATTTTGTTCATTTCAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.40% 7.60% 0.00% 0.00% NA
All Indica  2759 94.00% 6.00% 0.00% 0.00% NA
All Japonica  1512 87.80% 12.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 89.60% 10.40% 0.00% 0.00% NA
Indica Intermediate  786 92.20% 7.80% 0.00% 0.00% NA
Temperate Japonica  767 83.20% 16.80% 0.00% 0.00% NA
Tropical Japonica  504 92.10% 7.90% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0621702300 A -> G LOC_Os06g36830.1 upstream_gene_variant ; 2739.0bp to feature; MODIFIER silent_mutation Average:57.79; most accessible tissue: Minghui63 flower, score: 72.895 N N N N
vg0621702300 A -> G LOC_Os06g36840.1 intron_variant ; MODIFIER silent_mutation Average:57.79; most accessible tissue: Minghui63 flower, score: 72.895 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621702300 NA 8.35E-08 mr1104 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
vg0621702300 NA 2.87E-06 mr1182_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
vg0621702300 3.62E-06 3.62E-06 mr1282_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