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Detailed information for vg0416747657:

Variant ID: vg0416747657 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16747657
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: 128. )

Flanking Sequence (100 bp) in Reference Genome:


CTACGTATATTGATATGTAGATAATTTTTTTAAGAAACAAAATACAAACGCGCATACACTTTATACACGGGTGACTCACCGTCGACCGCACCCGTATTAA[G/A]
TCTAGAACTTAAACCCTTATACCACGGACGTCTCGCCGTTGAATACGAGCACCTATATTAAGTCTAGAACTTGAACCTGATGAGCCGGTTCTGTCACACG

Reverse complement sequence

CGTGTGACAGAACCGGCTCATCAGGTTCAAGTTCTAGACTTAATATAGGTGCTCGTATTCAACGGCGAGACGTCCGTGGTATAAGGGTTTAAGTTCTAGA[C/T]
TTAATACGGGTGCGGTCGACGGTGAGTCACCCGTGTATAAAGTGTATGCGCGTTTGTATTTTGTTTCTTAAAAAAATTATCTACATATCAATATACGTAG

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 95.40% 3.10% 1.50% 0.00% NA
All Indica  2759 94.40% 4.30% 1.30% 0.00% NA
All Japonica  1512 96.10% 1.70% 2.25% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 79.30% 15.10% 5.55% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.00% 0.38% 0.00% NA
Temperate Japonica  767 92.60% 3.30% 4.17% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0416747657 G -> A LOC_Os04g28290-LOC_Os04g28300 intergenic_region ; MODIFIER silent_mutation Average:50.68; most accessible tissue: Minghui63 root, score: 79.74 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416747657 1.44E-06 5.63E-06 mr1329_2 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
vg0416747657 6.84E-07 1.12E-06 mr1337_2 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
vg0416747657 3.36E-06 NA mr1342_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
vg0416747657 8.45E-06 8.45E-06 mr1369_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
vg0416747657 7.22E-06 7.22E-06 mr1453_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
vg0416747657 5.69E-07 1.64E-06 mr1524_2 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
vg0416747657 8.04E-06 8.05E-06 mr1652_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
vg0416747657 NA 2.83E-08 mr1864_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