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Detailed information for vg1003133816:

Variant ID: vg1003133816 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3133816
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, C: 0.28, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TACTCTCCCTCCTCTCTATCCATGCATGGATGCATGAATTCAAAATGAATTTTCTCCTAAACTACTTATCTAATATACTATCCGATAACACTCTTATATT[C/T]
GTTGTAATTAAATCTTCACGACAAGATATGGCGTGATTATGTTCTGATGTAAAAAAACATATGTTTTAGTCCGTTAATACTTAATGTTTCATAGCAACAT

Reverse complement sequence

ATGTTGCTATGAAACATTAAGTATTAACGGACTAAAACATATGTTTTTTTACATCAGAACATAATCACGCCATATCTTGTCGTGAAGATTTAATTACAAC[G/A]
AATATAAGAGTGTTATCGGATAGTATATTAGATAAGTAGTTTAGGAGAAAATTCATTTTGAATTCATGCATCCATGCATGGATAGAGAGGAGGGAGAGTA

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 80.20% 12.00% 0.47% 7.30% NA
All Indica  2759 83.30% 16.10% 0.22% 0.33% NA
All Japonica  1512 74.90% 2.40% 0.99% 21.63% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 80.70% 18.20% 0.00% 1.18% NA
Indica II  465 86.70% 12.90% 0.43% 0.00% NA
Indica III  913 81.80% 18.00% 0.22% 0.00% NA
Indica Intermediate  786 85.10% 14.40% 0.25% 0.25% NA
Temperate Japonica  767 63.50% 0.10% 1.56% 34.81% NA
Tropical Japonica  504 91.70% 6.90% 0.00% 1.39% NA
Japonica Intermediate  241 76.30% 0.40% 1.24% 21.99% NA
VI/Aromatic  96 42.70% 50.00% 1.04% 6.25% NA
Intermediate  90 81.10% 15.60% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003133816 C -> T LOC_Os10g06140-LOC_Os10g06160 intergenic_region ; MODIFIER silent_mutation Average:32.969; most accessible tissue: Callus, score: 55.669 N N N N
vg1003133816 C -> DEL N N silent_mutation Average:32.969; most accessible tissue: Callus, score: 55.669 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003133816 9.61E-07 2.32E-08 mr1538 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
vg1003133816 7.24E-09 1.71E-07 mr1547 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
vg1003133816 4.71E-10 1.33E-11 mr1547 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
vg1003133816 8.94E-10 7.80E-13 mr1709 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
vg1003133816 3.17E-10 6.49E-11 mr1709 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
vg1003133816 NA 5.15E-09 mr1538_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
vg1003133816 2.69E-09 4.05E-12 mr1547_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
vg1003133816 1.10E-11 1.34E-14 mr1547_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
vg1003133816 1.87E-14 3.36E-13 mr1709_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
vg1003133816 2.41E-12 3.71E-12 mr1709_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
vg1003133816 NA 4.15E-06 mr1721_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