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Detailed information for vg0131510210:

Variant ID: vg0131510210 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31510210
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGGCATTTGTGGGCGCATTACTCTGGCTGTGTTTAGTTCCATGCCAAAATTGAAAGTTTGAAGAGATTAGAACGATGCGATGGAAAAGTTAAAAATTT[G/A]
TGTGTAGGAAAGTTTGATGTGACGGAAAAGTTAAAAGTTTGAATAAAAAGGTTGGAATCTAAACAGGGCCTCTGTCCATTTTTCTTACAAATTATGGTTC

Reverse complement sequence

GAACCATAATTTGTAAGAAAAATGGACAGAGGCCCTGTTTAGATTCCAACCTTTTTATTCAAACTTTTAACTTTTCCGTCACATCAAACTTTCCTACACA[C/T]
AAATTTTTAACTTTTCCATCGCATCGTTCTAATCTCTTCAAACTTTCAATTTTGGCATGGAACTAAACACAGCCAGAGTAATGCGCCCACAAATGCCACA

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 95.70% 3.50% 0.47% 0.38% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 87.10% 10.30% 1.39% 1.19% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 63.50% 29.40% 3.57% 3.57% NA
Japonica Intermediate  241 96.70% 2.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 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
vg0131510210 G -> A LOC_Os01g54784.1 upstream_gene_variant ; 1324.0bp to feature; MODIFIER silent_mutation Average:60.573; most accessible tissue: Callus, score: 77.514 N N N N
vg0131510210 G -> A LOC_Os01g54760.1 downstream_gene_variant ; 4004.0bp to feature; MODIFIER silent_mutation Average:60.573; most accessible tissue: Callus, score: 77.514 N N N N
vg0131510210 G -> A LOC_Os01g54770.1 downstream_gene_variant ; 173.0bp to feature; MODIFIER silent_mutation Average:60.573; most accessible tissue: Callus, score: 77.514 N N N N
vg0131510210 G -> A LOC_Os01g54770-LOC_Os01g54784 intergenic_region ; MODIFIER silent_mutation Average:60.573; most accessible tissue: Callus, score: 77.514 N N N N
vg0131510210 G -> DEL N N silent_mutation Average:60.573; most accessible tissue: Callus, score: 77.514 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131510210 4.78E-07 NA mr1083_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
vg0131510210 2.96E-06 NA mr1104_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
vg0131510210 5.84E-07 NA mr1226_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