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Detailed information for vg0216113702:

Variant ID: vg0216113702 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16113702
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


GCCAAATTTCTACAGAAGGTATGTCTGTTGGATTATCTGGTGTGAAGGTATGGTTGTTGTTTGCTCTCACTTTGGTGCGGTTCCGTGGATTGGTGACCAC[G/A]
TATTATGCAAAGTTCTAGAGATTTTCACCTGATGTGCATTATTTTGATGGTATGACTACTGGGAATAGTGTGTTGTGGGAACCTAAACTATTGCCACTGT

Reverse complement sequence

ACAGTGGCAATAGTTTAGGTTCCCACAACACACTATTCCCAGTAGTCATACCATCAAAATAATGCACATCAGGTGAAAATCTCTAGAACTTTGCATAATA[C/T]
GTGGTCACCAATCCACGGAACCGCACCAAAGTGAGAGCAAACAACAACCATACCTTCACACCAGATAATCCAACAGACATACCTTCTGTAGAAATTTGGC

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 97.10% 2.10% 0.80% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 91.30% 6.20% 2.45% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 83.80% 11.90% 4.30% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 1.20% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0216113702 G -> A LOC_Os02g27360.1 downstream_gene_variant ; 1195.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Minghui63 flag leaf, score: 83.826 N N N N
vg0216113702 G -> A LOC_Os02g27360.2 downstream_gene_variant ; 1195.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Minghui63 flag leaf, score: 83.826 N N N N
vg0216113702 G -> A LOC_Os02g27350.1 intron_variant ; MODIFIER silent_mutation Average:57.906; most accessible tissue: Minghui63 flag leaf, score: 83.826 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216113702 NA 8.33E-07 mr1028 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
vg0216113702 1.50E-07 1.50E-07 mr1369 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
vg0216113702 3.80E-06 3.80E-06 mr1373 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
vg0216113702 NA 6.97E-07 mr1453 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
vg0216113702 NA 6.79E-08 mr1652 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
vg0216113702 NA 3.13E-06 mr1697 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