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Detailed information for vg0621432372:

Variant ID: vg0621432372 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21432372
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGTCATGATGCTCCGATTGTTTGAGCTATGTCTAACAAGCCGTAGAAAAATGAACAAAACAACCGAAACTAATTTATGGGTAACACTTGTATATTTG[A/T]
GTTGTTTGCGATTTAAAGGATAATACTGGAAAATAGACTACGATTAAAAAGCTACTAAATTTATGTTTCAAAATTTCAAACTTTGGCTGTGGCTGATAAG

Reverse complement sequence

CTTATCAGCCACAGCCAAAGTTTGAAATTTTGAAACATAAATTTAGTAGCTTTTTAATCGTAGTCTATTTTCCAGTATTATCCTTTAAATCGCAAACAAC[T/A]
CAAATATACAAGTGTTACCCATAAATTAGTTTCGGTTGTTTTGTTCATTTTTCTACGGCTTGTTAGACATAGCTCAAACAATCGGAGCATCATGACATAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.10% 44.70% 0.23% 0.00% NA
All Indica  2759 56.00% 43.70% 0.29% 0.00% NA
All Japonica  1512 64.40% 35.40% 0.20% 0.00% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 94.10% 5.90% 0.00% 0.00% NA
Indica II  465 68.00% 31.40% 0.65% 0.00% NA
Indica III  913 25.00% 74.80% 0.22% 0.00% NA
Indica Intermediate  786 56.10% 43.50% 0.38% 0.00% NA
Temperate Japonica  767 50.80% 48.80% 0.39% 0.00% NA
Tropical Japonica  504 81.70% 18.30% 0.00% 0.00% NA
Japonica Intermediate  241 71.40% 28.60% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0621432372 A -> T LOC_Os06g36500.1 downstream_gene_variant ; 3733.0bp to feature; MODIFIER silent_mutation Average:44.912; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N
vg0621432372 A -> T LOC_Os06g36490.1 intron_variant ; MODIFIER silent_mutation Average:44.912; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621432372 NA 8.46E-06 mr1027 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
vg0621432372 NA 3.56E-06 mr1215 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
vg0621432372 8.74E-07 8.73E-07 mr1327 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
vg0621432372 NA 8.48E-06 mr1382 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
vg0621432372 7.86E-06 7.86E-06 mr1464 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
vg0621432372 NA 3.42E-07 mr1583 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
vg0621432372 NA 9.78E-06 mr1602 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
vg0621432372 NA 8.08E-17 mr1583_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
vg0621432372 NA 1.23E-08 mr1583_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
vg0621432372 NA 1.67E-08 mr1850_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
vg0621432372 NA 2.16E-07 mr1877_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