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Detailed information for vg0621203049:

Variant ID: vg0621203049 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21203049
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.49, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GCGTGGTGTGGATGGTTAGGGGAGGGTTATGCGGAGGGTCTTGTCACGATTTCCCCCCCTTTGCAGTATCATGGTGATACTTCGGGGCATGGCGACATGT[A/G]
TGGAATCGTGTCTTGTGGGTACAGTTGTACACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTTATGGGCGATCAACCAGATTCACCGT

Reverse complement sequence

ACGGTGAATCTGGTTGATCGCCCATAACCGCGGGCACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACAACTGTACCCACAAGACACGATTCCA[T/C]
ACATGTCGCCATGCCCCGAAGTATCACCATGATACTGCAAAGGGGGGGAAATCGTGACAAGACCCTCCGCATAACCCTCCCCTAACCATCCACACCACGC

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 67.70% 32.30% 0.02% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 6.50% 93.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 2.90% 97.10% 0.00% 0.00% NA
Tropical Japonica  504 11.50% 88.50% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 56.20% 43.80% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 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
vg0621203049 A -> G LOC_Os06g36190.1 downstream_gene_variant ; 2534.0bp to feature; MODIFIER silent_mutation Average:25.141; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N
vg0621203049 A -> G LOC_Os06g36190-LOC_Os06g36210 intergenic_region ; MODIFIER silent_mutation Average:25.141; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621203049 2.46E-06 NA mr1100_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
vg0621203049 4.58E-06 NA mr1203_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
vg0621203049 NA 7.14E-10 mr1646_2 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