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Detailed information for vg0100791243:

Variant ID: vg0100791243 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 791243
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


ACAAGTCATCCTCATTGCAGGTAATGCAGATATTCCCTGTTCTTCAAATTCTCGCCTGTCAGCAACCAAGATTTTGTGTACTCTTGTTCCAATAAGAGTT[G/T]
CTTTGTTCCTTTTTCTTTTTGTTTCAAAAAGCAGATATTAGCTCACACCTTGCTTATCCTAATGGAACAAACTAATTTCATTTACTTTTACACAGCTACA

Reverse complement sequence

TGTAGCTGTGTAAAAGTAAATGAAATTAGTTTGTTCCATTAGGATAAGCAAGGTGTGAGCTAATATCTGCTTTTTGAAACAAAAAGAAAAAGGAACAAAG[C/A]
AACTCTTATTGGAACAAGAGTACACAAAATCTTGGTTGCTGACAGGCGAGAATTTGAAGAACAGGGAATATCTGCATTACCTGCAATGAGGATGACTTGT

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 33.10% 22.80% 2.26% 41.83% NA
All Indica  2759 27.90% 21.80% 2.83% 47.48% NA
All Japonica  1512 44.10% 28.70% 0.33% 26.85% NA
Aus  269 32.00% 4.10% 7.06% 56.88% NA
Indica I  595 1.80% 67.10% 2.18% 28.91% NA
Indica II  465 71.40% 4.10% 1.29% 23.23% NA
Indica III  913 15.20% 3.20% 3.29% 78.31% NA
Indica Intermediate  786 36.60% 19.60% 3.69% 40.08% NA
Temperate Japonica  767 68.30% 2.00% 0.39% 29.34% NA
Tropical Japonica  504 5.40% 77.20% 0.40% 17.06% NA
Japonica Intermediate  241 48.10% 12.40% 0.00% 39.42% NA
VI/Aromatic  96 3.10% 6.20% 3.12% 87.50% NA
Intermediate  90 41.10% 30.00% 2.22% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0100791243 G -> T LOC_Os01g02430.1 upstream_gene_variant ; 2624.0bp to feature; MODIFIER silent_mutation Average:34.858; most accessible tissue: Callus, score: 66.916 N N N N
vg0100791243 G -> T LOC_Os01g02460.1 upstream_gene_variant ; 3256.0bp to feature; MODIFIER silent_mutation Average:34.858; most accessible tissue: Callus, score: 66.916 N N N N
vg0100791243 G -> T LOC_Os01g02450.1 downstream_gene_variant ; 1845.0bp to feature; MODIFIER silent_mutation Average:34.858; most accessible tissue: Callus, score: 66.916 N N N N
vg0100791243 G -> T LOC_Os01g02440.1 intron_variant ; MODIFIER silent_mutation Average:34.858; most accessible tissue: Callus, score: 66.916 N N N N
vg0100791243 G -> DEL N N silent_mutation Average:34.858; most accessible tissue: Callus, score: 66.916 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0100791243 NA 7.42E-09 mr1059 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
vg0100791243 NA 4.97E-11 mr1143 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
vg0100791243 NA 8.83E-10 mr1167 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
vg0100791243 NA 1.11E-09 mr1535 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
vg0100791243 NA 1.28E-08 mr1593 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
vg0100791243 NA 1.22E-09 mr1675 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
vg0100791243 NA 8.71E-06 mr1686 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
vg0100791243 NA 9.90E-08 mr1739 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
vg0100791243 NA 1.18E-07 mr1739 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
vg0100791243 NA 9.93E-07 mr1950 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
vg0100791243 NA 1.11E-09 mr1969 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
vg0100791243 NA 2.59E-11 mr1995 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
vg0100791243 NA 1.68E-08 mr1167_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
vg0100791243 NA 7.68E-06 mr1360_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
vg0100791243 NA 2.51E-06 mr1378_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
vg0100791243 NA 1.74E-07 mr1383_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
vg0100791243 NA 2.42E-07 mr1458_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
vg0100791243 NA 5.70E-10 mr1593_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
vg0100791243 NA 7.05E-06 mr1726_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
vg0100791243 NA 1.43E-09 mr1739_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
vg0100791243 NA 2.46E-11 mr1794_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