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Detailed information for vg0622302745:

Variant ID: vg0622302745 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22302745
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ATATACTTCATAATCTTTATTAGTTGCTCTATGTAACTTGTAATCAGCTGGTTTTTACTGTTAGAAAGTAGCCGATAGAGTTAGATTTCGTTATTAATCT[A/T]
GATTATATTGTGTATCTACCATCTCTTAGAGATTTTCATTATCTTGTTTAGATCTTACAGTTATCTTTATACTTAATGCTGCATCGGTTGAGTTCGATCT

Reverse complement sequence

AGATCGAACTCAACCGATGCAGCATTAAGTATAAAGATAACTGTAAGATCTAAACAAGATAATGAAAATCTCTAAGAGATGGTAGATACACAATATAATC[T/A]
AGATTAATAACGAAATCTAACTCTATCGGCTACTTTCTAACAGTAAAAACCAGCTGATTACAAGTTACATAGAGCAACTAATAAAGATTATGAAGTATAT

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 57.40% 41.60% 0.57% 0.42% NA
All Indica  2759 32.60% 65.80% 0.91% 0.69% NA
All Japonica  1512 97.20% 2.70% 0.00% 0.07% NA
Aus  269 75.50% 24.50% 0.00% 0.00% NA
Indica I  595 17.10% 81.50% 0.84% 0.50% NA
Indica II  465 24.90% 72.70% 1.51% 0.86% NA
Indica III  913 46.70% 52.40% 0.33% 0.66% NA
Indica Intermediate  786 32.60% 65.40% 1.27% 0.76% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 95.20% 4.60% 0.00% 0.20% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 57.80% 40.00% 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
vg0622302745 A -> T LOC_Os06g37640.1 upstream_gene_variant ; 1715.0bp to feature; MODIFIER silent_mutation Average:44.197; most accessible tissue: Minghui63 young leaf, score: 59.171 N N N N
vg0622302745 A -> T LOC_Os06g37650.1 upstream_gene_variant ; 2346.0bp to feature; MODIFIER silent_mutation Average:44.197; most accessible tissue: Minghui63 young leaf, score: 59.171 N N N N
vg0622302745 A -> T LOC_Os06g37660.1 upstream_gene_variant ; 4377.0bp to feature; MODIFIER silent_mutation Average:44.197; most accessible tissue: Minghui63 young leaf, score: 59.171 N N N N
vg0622302745 A -> T LOC_Os06g37640-LOC_Os06g37650 intergenic_region ; MODIFIER silent_mutation Average:44.197; most accessible tissue: Minghui63 young leaf, score: 59.171 N N N N
vg0622302745 A -> DEL N N silent_mutation Average:44.197; most accessible tissue: Minghui63 young leaf, score: 59.171 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622302745 NA 3.44E-06 mr1037 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
vg0622302745 NA 1.03E-06 mr1044 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
vg0622302745 NA 1.10E-06 mr1058 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
vg0622302745 NA 6.95E-08 mr1064 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
vg0622302745 NA 2.76E-06 mr1066 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
vg0622302745 NA 2.19E-06 mr1069 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
vg0622302745 NA 1.67E-07 mr1075 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
vg0622302745 NA 1.71E-06 mr1077 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
vg0622302745 NA 2.10E-06 mr1149 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
vg0622302745 NA 2.33E-06 mr1155 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
vg0622302745 NA 2.22E-06 mr1202 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
vg0622302745 NA 2.36E-07 mr1237 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
vg0622302745 NA 2.10E-06 mr1285 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
vg0622302745 7.92E-06 NA mr1289 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
vg0622302745 1.25E-06 1.25E-06 mr1296 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
vg0622302745 NA 1.27E-12 mr1329 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
vg0622302745 NA 5.52E-12 mr1342 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
vg0622302745 NA 2.92E-06 mr1408 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
vg0622302745 NA 1.14E-06 mr1534 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
vg0622302745 NA 7.73E-07 mr1574 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
vg0622302745 NA 5.78E-06 mr1741 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
vg0622302745 NA 5.08E-10 mr1746 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
vg0622302745 NA 6.48E-07 mr1746 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
vg0622302745 NA 6.83E-07 mr1749 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
vg0622302745 NA 4.82E-09 mr1770 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
vg0622302745 NA 5.88E-06 mr1795 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
vg0622302745 NA 1.68E-06 mr1887 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
vg0622302745 NA 4.50E-06 mr1981 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
vg0622302745 NA 5.60E-06 mr1981 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
vg0622302745 NA 1.41E-08 mr1322_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
vg0622302745 NA 7.52E-15 mr1333_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
vg0622302745 NA 2.79E-10 mr1338_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
vg0622302745 NA 4.06E-15 mr1686_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