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Detailed information for vg1020006876:

Variant ID: vg1020006876 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 20006876
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: 218. )

Flanking Sequence (100 bp) in Reference Genome:


CTGCCAAATAAACCATTATTAAGATTTTATAGCTTTAAAATTTTAAAGTCCAATTAACAAAGTTAAATTTTGAGGAAGCCAAAGATTACTTCGTCCGTTT[C/T]
AAAATGTAGTTATTTTTGAGGTTGGCATGAGTATTAAAAAAAGTATGTGAGAATGATTGGAGGAAGTGTGTAATTGGTTAAAAAGATAAAGTAGGTGAAG

Reverse complement sequence

CTTCACCTACTTTATCTTTTTAACCAATTACACACTTCCTCCAATCATTCTCACATACTTTTTTTAATACTCATGCCAACCTCAAAAATAACTACATTTT[G/A]
AAACGGACGAAGTAATCTTTGGCTTCCTCAAAATTTAACTTTGTTAATTGGACTTTAAAATTTTAAAGCTATAAAATCTTAATAATGGTTTATTTGGCAG

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 90.10% 9.90% 0.04% 0.00% NA
All Indica  2759 91.30% 8.70% 0.04% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 30.50% 69.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 74.60% 25.40% 0.00% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 86.50% 13.40% 0.13% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 15.60% 1.04% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1020006876 C -> T LOC_Os10g37340.1 upstream_gene_variant ; 2277.0bp to feature; MODIFIER silent_mutation Average:45.817; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg1020006876 C -> T LOC_Os10g37350.1 upstream_gene_variant ; 4623.0bp to feature; MODIFIER silent_mutation Average:45.817; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg1020006876 C -> T LOC_Os10g37330.1 downstream_gene_variant ; 4919.0bp to feature; MODIFIER silent_mutation Average:45.817; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg1020006876 C -> T LOC_Os10g37340-LOC_Os10g37350 intergenic_region ; MODIFIER silent_mutation Average:45.817; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1020006876 NA 9.69E-06 mr1188 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
vg1020006876 NA 1.19E-06 mr1188_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
vg1020006876 1.87E-07 4.39E-07 mr1521_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
vg1020006876 NA 4.22E-17 mr1961_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