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Detailed information for vg0400966446:

Variant ID: vg0400966446 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 966446
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TAAAAAAAAGTCAACAGCGTCATCTATTAAAAATATGAAGGTAGTAATAATTTTCCTATGTACCTAGCAGTTGCATTACTATCCACTTACTAGCCTACGC[A/C]
CCTAATTAGTTTATCTTATTATGTGTATAGGCGTATATATTGCTCATGCCCATATTATTTCTGTGTGGGACCTGTGTTTTACGGCTAAATGTAAAAAAAA

Reverse complement sequence

TTTTTTTTACATTTAGCCGTAAAACACAGGTCCCACACAGAAATAATATGGGCATGAGCAATATATACGCCTATACACATAATAAGATAAACTAATTAGG[T/G]
GCGTAGGCTAGTAAGTGGATAGTAATGCAACTGCTAGGTACATAGGAAAATTATTACTACCTTCATATTTTTAATAGATGACGCTGTTGACTTTTTTTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.60% 44.70% 0.25% 0.40% NA
All Indica  2759 62.70% 36.30% 0.29% 0.69% NA
All Japonica  1512 39.00% 60.90% 0.07% 0.00% NA
Aus  269 75.80% 23.80% 0.37% 0.00% NA
Indica I  595 79.20% 20.80% 0.00% 0.00% NA
Indica II  465 54.40% 44.70% 0.00% 0.86% NA
Indica III  913 66.00% 32.00% 0.66% 1.31% NA
Indica Intermediate  786 51.30% 48.10% 0.25% 0.38% NA
Temperate Japonica  767 62.30% 37.70% 0.00% 0.00% NA
Tropical Japonica  504 15.10% 84.90% 0.00% 0.00% NA
Japonica Intermediate  241 14.90% 84.60% 0.41% 0.00% NA
VI/Aromatic  96 17.70% 80.20% 2.08% 0.00% NA
Intermediate  90 45.60% 54.40% 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
vg0400966446 A -> C LOC_Os04g02570.1 downstream_gene_variant ; 697.0bp to feature; MODIFIER silent_mutation Average:43.678; most accessible tissue: Callus, score: 79.25 N N N N
vg0400966446 A -> C LOC_Os04g02580.1 downstream_gene_variant ; 1521.0bp to feature; MODIFIER silent_mutation Average:43.678; most accessible tissue: Callus, score: 79.25 N N N N
vg0400966446 A -> C LOC_Os04g02560-LOC_Os04g02570 intergenic_region ; MODIFIER silent_mutation Average:43.678; most accessible tissue: Callus, score: 79.25 N N N N
vg0400966446 A -> DEL N N silent_mutation Average:43.678; most accessible tissue: Callus, score: 79.25 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400966446 NA 9.92E-06 mr1182 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
vg0400966446 NA 2.61E-06 mr1650 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
vg0400966446 7.18E-06 7.06E-07 mr1242_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
vg0400966446 NA 9.91E-06 mr1631_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
vg0400966446 NA 6.77E-06 mr1835_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
vg0400966446 2.64E-06 3.50E-09 mr1904_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