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Detailed information for vg0301938071:

Variant ID: vg0301938071 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1938071
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTAGGCTATCTATTGGACGGAGGTGTTTTTTCACTTCCTATTTTCAGTTTAGGAAACCAAAAACGAATTTTTAAAAGAAAATTATAGATAATCTGTTG[G/A]
TGATGCTCTTAGTCAACTTGTATCATGAAATCCTCTGTTTCGTAACCGGTTTTCCTTATTGTCATGCATTAATTAGTGCATTACCACATGATCTAAAAGG

Reverse complement sequence

CCTTTTAGATCATGTGGTAATGCACTAATTAATGCATGACAATAAGGAAAACCGGTTACGAAACAGAGGATTTCATGATACAAGTTGACTAAGAGCATCA[C/T]
CAACAGATTATCTATAATTTTCTTTTAAAAATTCGTTTTTGGTTTCCTAAACTGAAAATAGGAAGTGAAAAAACACCTCCGTCCAATAGATAGCCTAAAT

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 97.90% 1.10% 0.99% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 93.70% 3.30% 3.04% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 88.10% 6.50% 5.35% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 0.00% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg0301938071 G -> A LOC_Os03g04210.1 downstream_gene_variant ; 801.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301938071 G -> A LOC_Os03g04220.1 downstream_gene_variant ; 131.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301938071 G -> A LOC_Os03g04210-LOC_Os03g04220 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301938071 NA 2.70E-08 mr1062 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
vg0301938071 NA 5.55E-07 mr1585 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
vg0301938071 4.05E-06 NA mr1002_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
vg0301938071 7.74E-06 7.38E-09 mr1062_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