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Detailed information for vg0400995844:

Variant ID: vg0400995844 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 995844
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CGTGTAGCCGACGCAGCCCCTGTCAGAAAAAAGAGGGTGGCGATGCGCCAAGAGTAATTATATTGTCTTGACAATTCCTATCGACCGATTCTAAGATGCT[G/A]
AAGTCGATAGTGACTCTAAGCCGATGATAACACCGGGGTTTACCAAATTTTAACGTTAACACCCGGTCATCTCCACCGCGCCGCCCCAACCAGCCAGGGT

Reverse complement sequence

ACCCTGGCTGGTTGGGGCGGCGCGGTGGAGATGACCGGGTGTTAACGTTAAAATTTGGTAAACCCCGGTGTTATCATCGGCTTAGAGTCACTATCGACTT[C/T]
AGCATCTTAGAATCGGTCGATAGGAATTGTCAAGACAATATAATTACTCTTGGCGCATCGCCACCCTCTTTTTTCTGACAGGGGCTGCGTCGGCTACACG

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 94.20% 5.50% 0.28% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 89.40% 9.70% 0.86% 0.00% NA
Aus  269 78.80% 21.20% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.50% 0.00% 0.00% NA
Temperate Japonica  767 83.40% 15.00% 1.56% 0.00% NA
Tropical Japonica  504 95.60% 4.40% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.10% 0.41% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0400995844 G -> A LOC_Os04g02640.1 upstream_gene_variant ; 1460.0bp to feature; MODIFIER silent_mutation Average:73.402; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0400995844 G -> A LOC_Os04g02630.1 downstream_gene_variant ; 3321.0bp to feature; MODIFIER silent_mutation Average:73.402; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0400995844 G -> A LOC_Os04g02650.1 downstream_gene_variant ; 3796.0bp to feature; MODIFIER silent_mutation Average:73.402; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0400995844 G -> A LOC_Os04g02630-LOC_Os04g02640 intergenic_region ; MODIFIER silent_mutation Average:73.402; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400995844 2.47E-06 NA mr1166 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
vg0400995844 2.41E-07 3.46E-10 mr1585 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
vg0400995844 1.96E-06 NA mr1586 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
vg0400995844 2.81E-07 9.61E-09 mr1585_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