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Detailed information for vg1107386372:

Variant ID: vg1107386372 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7386372
Reference Allele: CAlternative Allele: T
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: 65. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCACGGTAGAGCATCCCTCCGTTCTCCCTCCTCGATCCCTCTCCCCCCTTAGAGTTGGTGGTAGCGCTCGTAGCACTCCCCGTAGCCTGTAGGCGCCG[C/T]
ACCAAGTCTCGCCACCGCTTGGCACGGCATCGCTGCCGTTGCCGCTCGCCGCCGCAAGCCACCGCTCGTCGCCAGCCTCTCTCTGCGTAGCTCTGTCCGA

Reverse complement sequence

TCGGACAGAGCTACGCAGAGAGAGGCTGGCGACGAGCGGTGGCTTGCGGCGGCGAGCGGCAACGGCAGCGATGCCGTGCCAAGCGGTGGCGAGACTTGGT[G/A]
CGGCGCCTACAGGCTACGGGGAGTGCTACGAGCGCTACCACCAACTCTAAGGGGGGAGAGGGATCGAGGAGGGAGAACGGAGGGATGCTCTACCGTGGCG

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 38.60% 27.00% 0.68% 33.69% NA
All Indica  2759 4.90% 44.80% 0.87% 49.44% NA
All Japonica  1512 91.70% 0.70% 0.26% 7.34% NA
Aus  269 63.20% 2.60% 0.37% 33.83% NA
Indica I  595 2.90% 22.90% 1.34% 72.94% NA
Indica II  465 1.50% 67.50% 0.43% 30.54% NA
Indica III  913 3.90% 52.90% 0.66% 42.50% NA
Indica Intermediate  786 9.50% 38.50% 1.02% 50.89% NA
Temperate Japonica  767 96.50% 0.40% 0.26% 2.87% NA
Tropical Japonica  504 89.30% 1.40% 0.40% 8.93% NA
Japonica Intermediate  241 81.30% 0.40% 0.00% 18.26% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 45.60% 24.40% 3.33% 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
vg1107386372 C -> T LOC_Os11g13480.1 upstream_gene_variant ; 2353.0bp to feature; MODIFIER silent_mutation Average:47.122; most accessible tissue: Minghui63 flag leaf, score: 82.75 N N N N
vg1107386372 C -> T LOC_Os11g13480-LOC_Os11g13490 intergenic_region ; MODIFIER silent_mutation Average:47.122; most accessible tissue: Minghui63 flag leaf, score: 82.75 N N N N
vg1107386372 C -> DEL N N silent_mutation Average:47.122; most accessible tissue: Minghui63 flag leaf, score: 82.75 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107386372 NA 3.37E-06 mr1011 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
vg1107386372 NA 1.51E-07 mr1215_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
vg1107386372 NA 1.49E-09 mr1302_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
vg1107386372 NA 7.58E-08 mr1376_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
vg1107386372 NA 9.88E-07 mr1407_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
vg1107386372 NA 2.61E-08 mr1431_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
vg1107386372 NA 3.89E-08 mr1604_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
vg1107386372 NA 6.08E-07 mr1609_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
vg1107386372 NA 6.58E-06 mr1767_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
vg1107386372 NA 6.97E-09 mr1824_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
vg1107386372 NA 1.64E-11 mr1830_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
vg1107386372 NA 2.75E-06 mr1837_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
vg1107386372 NA 9.79E-07 mr1869_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
vg1107386372 NA 2.54E-08 mr1885_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
vg1107386372 NA 5.48E-06 mr1959_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