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Detailed information for vg0507826953:

Variant ID: vg0507826953 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7826953
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTTGACCTCGAGTTGGCACCAGTGATGGAGGTTAACGATGACGACGAGGTGGGGACAACCACTTGCGGAGATGAGAAGGAGACGATTAGTTATGGATC[T/A]
AGAGGCGGCGACGGCCGGTCGACCTTGAGCTGGCGCCCGTGATGGAGGTGAAAGACGATGACAGGGTGGGGTGACCGCTCATGGTGACGAGAAGGAGGCA

Reverse complement sequence

TGCCTCCTTCTCGTCACCATGAGCGGTCACCCCACCCTGTCATCGTCTTTCACCTCCATCACGGGCGCCAGCTCAAGGTCGACCGGCCGTCGCCGCCTCT[A/T]
GATCCATAACTAATCGTCTCCTTCTCATCTCCGCAAGTGGTTGTCCCCACCTCGTCGTCATCGTTAACCTCCATCACTGGTGCCAACTCGAGGTCAACTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 1.20% 1.14% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.80% 3.70% 3.51% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 88.70% 5.20% 6.13% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 91.70% 6.60% 1.66% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0507826953 T -> A LOC_Os05g14010-LOC_Os05g14030 intergenic_region ; MODIFIER silent_mutation Average:64.673; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507826953 4.69E-10 4.69E-10 mr1024_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
vg0507826953 2.46E-07 5.61E-10 mr1565_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
vg0507826953 1.30E-06 1.30E-06 mr1915_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
vg0507826953 NA 5.99E-06 mr1922_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
vg0507826953 4.54E-07 4.54E-07 mr1940_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