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Detailed information for vg0621412586:

Variant ID: vg0621412586 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21412586
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCCGTCCCGTCAGGAGGATGTTCGGAGGACAACCGTGCAAATCTCCGTCCATTTATGAAGAGAAGAAAAGTCCAGTTTGGAAAGAGAGGGGTGCATGTG[G/C]
TATCCCCTTGAAGTATAAAAGGAGGACCCTGCCCATGGGGAAGGGGGATGATCTTTTCCAGATTCAGTAGCTAGAAGAAAAGGGGGAGGTTGGCTCACAC

Reverse complement sequence

GTGTGAGCCAACCTCCCCCTTTTCTTCTAGCTACTGAATCTGGAAAAGATCATCCCCCTTCCCCATGGGCAGGGTCCTCCTTTTATACTTCAAGGGGATA[C/G]
CACATGCACCCCTCTCTTTCCAAACTGGACTTTTCTTCTCTTCATAAATGGACGGAGATTTGCACGGTTGTCCTCCGAACATCCTCCTGACGGGACGGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.10% 0.30% 5.18% 11.43% NA
All Indica  2759 84.30% 0.50% 8.05% 7.18% NA
All Japonica  1512 89.40% 0.00% 0.66% 9.99% NA
Aus  269 27.90% 0.00% 2.97% 69.14% NA
Indica I  595 80.20% 0.80% 13.78% 5.21% NA
Indica II  465 84.70% 0.40% 6.88% 7.96% NA
Indica III  913 87.60% 0.20% 3.83% 8.32% NA
Indica Intermediate  786 83.20% 0.60% 9.29% 6.87% NA
Temperate Japonica  767 81.70% 0.00% 0.78% 17.47% NA
Tropical Japonica  504 98.40% 0.00% 0.79% 0.79% NA
Japonica Intermediate  241 94.60% 0.00% 0.00% 5.39% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 91.10% 0.00% 3.33% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0621412586 G -> C LOC_Os06g36470.1 downstream_gene_variant ; 2263.0bp to feature; MODIFIER silent_mutation Average:26.751; most accessible tissue: Minghui63 root, score: 45.031 N N N N
vg0621412586 G -> C LOC_Os06g36480.1 downstream_gene_variant ; 1588.0bp to feature; MODIFIER silent_mutation Average:26.751; most accessible tissue: Minghui63 root, score: 45.031 N N N N
vg0621412586 G -> C LOC_Os06g36470-LOC_Os06g36480 intergenic_region ; MODIFIER silent_mutation Average:26.751; most accessible tissue: Minghui63 root, score: 45.031 N N N N
vg0621412586 G -> DEL N N silent_mutation Average:26.751; most accessible tissue: Minghui63 root, score: 45.031 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621412586 3.09E-06 NA mr1184_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
vg0621412586 5.26E-06 3.67E-06 mr1184_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
vg0621412586 NA 2.85E-08 mr1212_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
vg0621412586 8.83E-06 NA mr1284_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
vg0621412586 5.50E-06 NA mr1374_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
vg0621412586 3.12E-06 3.12E-06 mr1374_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
vg0621412586 5.05E-06 5.04E-06 mr1412_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
vg0621412586 7.25E-06 7.25E-06 mr1412_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
vg0621412586 NA 9.89E-06 mr1417_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
vg0621412586 3.34E-06 3.34E-06 mr1440_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
vg0621412586 NA 9.54E-06 mr1641_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
vg0621412586 6.44E-06 3.93E-06 mr1683_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
vg0621412586 8.06E-06 1.32E-06 mr1747_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
vg0621412586 2.41E-06 2.41E-06 mr1747_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
vg0621412586 3.30E-06 NA mr1811_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
vg0621412586 7.50E-06 4.36E-06 mr1811_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
vg0621412586 2.45E-06 5.91E-06 mr1816_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
vg0621412586 4.26E-06 4.26E-06 mr1816_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
vg0621412586 NA 2.65E-06 mr1831_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
vg0621412586 3.52E-06 3.92E-06 mr1831_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
vg0621412586 NA 3.50E-06 mr1840_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
vg0621412586 NA 4.69E-06 mr1856_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