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Detailed information for vg1100141615:

Variant ID: vg1100141615 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 141615
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTCTTAACTGGCCGCTACATGTCTATGGCTTGGTTGCCACCAGGGATTCTGTAGATCAAAAGCGCAACCTTCTTTTCAAGCGCACAAGGGATAATTGT[T/C]
AACTTCTGACTCCACAGGTTAGATATCTTGTAATTTCCTCTTAACTTTATTGTTTCTCATTTTTCTTGGAGCTTGAAGTCCTCAACCTACTACAATTTCT

Reverse complement sequence

AGAAATTGTAGTAGGTTGAGGACTTCAAGCTCCAAGAAAAATGAGAAACAATAAAGTTAAGAGGAAATTACAAGATATCTAACCTGTGGAGTCAGAAGTT[A/G]
ACAATTATCCCTTGTGCGCTTGAAAAGAAGGTTGCGCTTTTGATCTACAGAATCCCTGGTGGCAACCAAGCCATAGACATGTAGCGGCCAGTTAAGACCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.30% 43.40% 0.23% 0.04% NA
All Indica  2759 87.50% 12.10% 0.33% 0.07% NA
All Japonica  1512 1.50% 98.50% 0.00% 0.00% NA
Aus  269 67.70% 32.30% 0.00% 0.00% NA
Indica I  595 98.20% 1.50% 0.34% 0.00% NA
Indica II  465 54.60% 45.20% 0.22% 0.00% NA
Indica III  913 95.70% 4.10% 0.11% 0.11% NA
Indica Intermediate  786 89.30% 9.90% 0.64% 0.13% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 31.10% 66.70% 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
vg1100141615 T -> DEL N N silent_mutation Average:55.827; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg1100141615 T -> C LOC_Os11g01250.1 upstream_gene_variant ; 1297.0bp to feature; MODIFIER silent_mutation Average:55.827; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg1100141615 T -> C LOC_Os11g01240.1 downstream_gene_variant ; 2656.0bp to feature; MODIFIER silent_mutation Average:55.827; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg1100141615 T -> C LOC_Os11g01270.1 downstream_gene_variant ; 2550.0bp to feature; MODIFIER silent_mutation Average:55.827; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg1100141615 T -> C LOC_Os11g01260.1 intron_variant ; MODIFIER silent_mutation Average:55.827; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100141615 NA 3.72E-06 mr1032 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
vg1100141615 NA 2.24E-11 mr1609 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
vg1100141615 NA 2.31E-06 mr1835 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
vg1100141615 NA 1.20E-10 mr1889 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
vg1100141615 NA 1.31E-08 mr1896 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
vg1100141615 NA 3.81E-09 mr1903 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
vg1100141615 NA 5.58E-11 mr1904 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
vg1100141615 NA 1.17E-14 mr1907 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
vg1100141615 NA 3.85E-11 mr1934 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
vg1100141615 NA 2.92E-09 mr1935 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
vg1100141615 NA 4.01E-06 mr1332_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
vg1100141615 NA 2.25E-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
vg1100141615 NA 2.50E-11 mr1520_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
vg1100141615 NA 3.03E-09 mr1835_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
vg1100141615 NA 9.44E-15 mr1889_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
vg1100141615 NA 5.99E-09 mr1896_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
vg1100141615 NA 4.93E-13 mr1904_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
vg1100141615 NA 1.00E-14 mr1907_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
vg1100141615 NA 4.83E-11 mr1934_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