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Detailed information for vg0918112528:

Variant ID: vg0918112528 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18112528
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATTTGCATGATGTTACTATGTAAATTGCACCATGAACTGTTTGGCTGCCAATAAAGGTTAACACATTTTTTTTTTCGAATAGAGAGATCAAAGAAGG[C/T]
TCAACAAATCTAGTGCTTTTAAAATAGATTGGGAAAACAGAGTTCTGTAAAAAAAAACGGAGTTGCAAAATATATTCTTCTATGAAAAATTGAAGGACTA

Reverse complement sequence

TAGTCCTTCAATTTTTCATAGAAGAATATATTTTGCAACTCCGTTTTTTTTTACAGAACTCTGTTTTCCCAATCTATTTTAAAAGCACTAGATTTGTTGA[G/A]
CCTTCTTTGATCTCTCTATTCGAAAAAAAAAATGTGTTAACCTTTATTGGCAGCCAAACAGTTCATGGTGCAATTTACATAGTAACATCATGCAAATCAA

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 57.00% 43.00% 0.06% 0.00% NA
All Indica  2759 27.00% 72.90% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 58.30% 41.70% 0.00% 0.00% NA
Indica II  465 9.70% 90.30% 0.00% 0.00% NA
Indica III  913 8.30% 91.60% 0.11% 0.00% NA
Indica Intermediate  786 35.10% 64.60% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0918112528 C -> T LOC_Os09g29790.1 upstream_gene_variant ; 3215.0bp to feature; MODIFIER silent_mutation Average:35.513; most accessible tissue: Callus, score: 80.523 N N N N
vg0918112528 C -> T LOC_Os09g29810.1 upstream_gene_variant ; 2597.0bp to feature; MODIFIER silent_mutation Average:35.513; most accessible tissue: Callus, score: 80.523 N N N N
vg0918112528 C -> T LOC_Os09g29800.1 intron_variant ; MODIFIER silent_mutation Average:35.513; most accessible tissue: Callus, score: 80.523 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918112528 NA 4.11E-15 mr1138 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
vg0918112528 NA 2.05E-08 mr1138 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
vg0918112528 NA 3.47E-07 mr1716 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
vg0918112528 NA 9.34E-08 mr1728 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
vg0918112528 NA 2.24E-06 mr1860 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
vg0918112528 NA 4.20E-15 mr1138_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
vg0918112528 NA 4.33E-08 mr1138_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
vg0918112528 NA 4.49E-14 mr1330_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
vg0918112528 NA 4.99E-18 mr1352_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
vg0918112528 NA 6.38E-09 mr1527_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
vg0918112528 NA 1.50E-08 mr1728_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
vg0918112528 NA 5.25E-07 mr1834_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
vg0918112528 NA 3.93E-07 mr1860_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