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Detailed information for vg0506837520:

Variant ID: vg0506837520 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6837520
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGAAAATAAAATAAATTGTGAAAACTCGCGATACAGGGGTTGTGCCTGTGTGGCGTTGTCCCGTATTTGCATATAAGGACCAATTCATGTGGGAAATT[C/T]
ATCCGAGCATATAACAAGTGCGACCACACGGGTAGAATGAGACGCTCTTGGTTGAGTAAATAGCAAACCAGGGAAGCCTTGATGCCAAGAGACAAGTGGA

Reverse complement sequence

TCCACTTGTCTCTTGGCATCAAGGCTTCCCTGGTTTGCTATTTACTCAACCAAGAGCGTCTCATTCTACCCGTGTGGTCGCACTTGTTATATGCTCGGAT[G/A]
AATTTCCCACATGAATTGGTCCTTATATGCAAATACGGGACAACGCCACACAGGCACAACCCCTGTATCGCGAGTTTTCACAATTTATTTTATTTTCAAA

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 89.00% 11.00% 0.02% 0.00% NA
All Indica  2759 81.70% 18.20% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 70.80% 29.20% 0.00% 0.00% NA
Indica III  913 74.30% 25.70% 0.00% 0.00% NA
Indica Intermediate  786 87.20% 12.70% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 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 92.20% 7.80% 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
vg0506837520 C -> T LOC_Os05g11960.1 upstream_gene_variant ; 1154.0bp to feature; MODIFIER silent_mutation Average:46.078; most accessible tissue: Callus, score: 61.805 N N N N
vg0506837520 C -> T LOC_Os05g11970.1 upstream_gene_variant ; 1273.0bp to feature; MODIFIER silent_mutation Average:46.078; most accessible tissue: Callus, score: 61.805 N N N N
vg0506837520 C -> T LOC_Os05g11960-LOC_Os05g11970 intergenic_region ; MODIFIER silent_mutation Average:46.078; most accessible tissue: Callus, score: 61.805 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506837520 1.13E-68 2.91E-120 mr1039 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
vg0506837520 2.81E-52 2.26E-86 mr1039 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
vg0506837520 1.12E-24 3.83E-41 mr1632 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
vg0506837520 1.22E-20 5.93E-28 mr1632 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
vg0506837520 NA 9.54E-06 mr1873 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
vg0506837520 8.18E-82 1.57E-129 mr1039_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
vg0506837520 1.49E-58 4.77E-90 mr1039_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
vg0506837520 9.98E-12 2.08E-19 mr1514_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
vg0506837520 2.48E-10 8.59E-11 mr1514_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
vg0506837520 3.02E-44 4.12E-67 mr1632_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
vg0506837520 2.66E-34 2.02E-47 mr1632_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
vg0506837520 8.19E-11 NA mr1873_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
vg0506837520 1.72E-09 9.13E-12 mr1873_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