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Detailed information for vg1118143847:

Variant ID: vg1118143847 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18143847
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.14, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CTTAAACCGTGCACTCAAGTGGTTTCGCTGAAGTGGCATCCTAGTCAGCAAAAAAAAAATTAAAAAAGTATTTGGGACATGGAGCTCAAGCTCACCTCCG[C/T]
AGCCGACTCGGCCTCCACCGGTCCTTTTCTCCCACTGCCGCCGTCGCGCCGGCCACCTCCTCTCCCGCCGCTGCCATCACGCCGGCCGCCTCCTCTCCTT

Reverse complement sequence

AAGGAGAGGAGGCGGCCGGCGTGATGGCAGCGGCGGGAGAGGAGGTGGCCGGCGCGACGGCGGCAGTGGGAGAAAAGGACCGGTGGAGGCCGAGTCGGCT[G/A]
CGGAGGTGAGCTTGAGCTCCATGTCCCAAATACTTTTTTAATTTTTTTTTTGCTGACTAGGATGCCACTTCAGCGAAACCACTTGAGTGCACGGTTTAAG

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 56.60% 36.30% 0.30% 6.75% NA
All Indica  2759 58.40% 39.80% 0.47% 1.27% NA
All Japonica  1512 58.10% 23.80% 0.07% 17.99% NA
Aus  269 18.60% 80.30% 0.00% 1.12% NA
Indica I  595 54.50% 45.00% 0.50% 0.00% NA
Indica II  465 81.10% 15.90% 0.86% 2.15% NA
Indica III  913 50.80% 47.00% 0.22% 1.97% NA
Indica Intermediate  786 56.90% 41.70% 0.51% 0.89% NA
Temperate Japonica  767 94.50% 2.90% 0.00% 2.61% NA
Tropical Japonica  504 10.10% 41.10% 0.20% 48.61% NA
Japonica Intermediate  241 42.70% 54.40% 0.00% 2.90% NA
VI/Aromatic  96 77.10% 21.90% 0.00% 1.04% NA
Intermediate  90 68.90% 22.20% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1118143847 C -> T LOC_Os11g31160.1 upstream_gene_variant ; 306.0bp to feature; MODIFIER silent_mutation Average:64.507; most accessible tissue: Zhenshan97 young leaf, score: 85.364 N N N N
vg1118143847 C -> T LOC_Os11g31150-LOC_Os11g31160 intergenic_region ; MODIFIER silent_mutation Average:64.507; most accessible tissue: Zhenshan97 young leaf, score: 85.364 N N N N
vg1118143847 C -> DEL N N silent_mutation Average:64.507; most accessible tissue: Zhenshan97 young leaf, score: 85.364 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118143847 NA 9.47E-06 mr1579 Jap_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
vg1118143847 NA 2.50E-09 mr1042_2 Jap_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
vg1118143847 NA 1.98E-06 mr1043_2 Jap_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
vg1118143847 NA 4.14E-07 mr1047_2 Jap_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
vg1118143847 NA 4.31E-06 mr1091_2 Jap_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
vg1118143847 NA 1.17E-06 mr1115_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
vg1118143847 NA 2.68E-08 mr1189_2 Jap_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
vg1118143847 NA 8.84E-06 mr1359_2 Jap_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
vg1118143847 NA 4.94E-06 mr1479_2 Jap_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
vg1118143847 NA 3.15E-08 mr1482_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
vg1118143847 NA 4.08E-10 mr1502_2 Jap_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
vg1118143847 NA 5.25E-10 mr1543_2 Jap_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
vg1118143847 NA 6.26E-06 mr1550_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
vg1118143847 NA 4.19E-09 mr1680_2 Jap_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
vg1118143847 NA 2.09E-06 mr1729_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
vg1118143847 NA 5.96E-06 mr1736_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
vg1118143847 NA 6.44E-06 mr1740_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
vg1118143847 NA 2.54E-09 mr1742_2 Jap_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
vg1118143847 NA 1.31E-06 mr1763_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
vg1118143847 NA 3.81E-10 mr1871_2 Jap_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
vg1118143847 NA 3.88E-07 mr1892_2 Jap_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