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Detailed information for vg0204625031:

Variant ID: vg0204625031 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4625031
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTATTGTTTAGTTGGGAAAAAAATTTGGGGTTGGTTGTCACATCAGATATACGGATACACATTTGAAGTAATAAAGTAATAATAAAACAAATTTCACTA[G/T]
AAAACCGCGAAATGAATTTATTAAACCTAATTAATCATCATTAGCAAATGTTTACTGTAGCATCACATTGTCAAATCATGGTGCAATTAGTCTTATAAGA

Reverse complement sequence

TCTTATAAGACTAATTGCACCATGATTTGACAATGTGATGCTACAGTAAACATTTGCTAATGATGATTAATTAGGTTTAATAAATTCATTTCGCGGTTTT[C/A]
TAGTGAAATTTGTTTTATTATTACTTTATTACTTCAAATGTGTATCCGTATATCTGATGTGACAACCAACCCCAAATTTTTTTCCCAACTAAACAATACC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 3.90% 0.04% 0.00% NA
All Indica  2759 93.50% 6.50% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 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 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 88.80% 11.20% 0.00% 0.00% NA
Indica Intermediate  786 92.10% 7.90% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 4.40% 2.22% 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
vg0204625031 G -> T LOC_Os02g08544.1 upstream_gene_variant ; 364.0bp to feature; MODIFIER silent_mutation Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N
vg0204625031 G -> T LOC_Os02g08544.2 upstream_gene_variant ; 364.0bp to feature; MODIFIER silent_mutation Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N
vg0204625031 G -> T LOC_Os02g08544.3 upstream_gene_variant ; 1753.0bp to feature; MODIFIER silent_mutation Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N
vg0204625031 G -> T LOC_Os02g08540.1 downstream_gene_variant ; 2920.0bp to feature; MODIFIER silent_mutation Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N
vg0204625031 G -> T LOC_Os02g09050.1 downstream_gene_variant ; 4563.0bp to feature; MODIFIER silent_mutation Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N
vg0204625031 G -> T LOC_Os02g08540-LOC_Os02g08544 intergenic_region ; MODIFIER silent_mutation Average:69.109; most accessible tissue: Minghui63 panicle, score: 87.951 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204625031 4.32E-06 1.91E-06 mr1120_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
vg0204625031 9.75E-06 NA mr1123_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
vg0204625031 4.35E-06 6.52E-06 mr1247_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