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Detailed information for vg0624609971:

Variant ID: vg0624609971 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24609971
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCTAGGTTTTAGAGCTTTTCCAGATTCTCAGAAGCTGGCTACCAAACAACTGCTTCTCAGAATCTAAAGCTTCCCCAAACAGGCCCAAAGTTTGTCTT[C/T]
ATTAGAGTTCACATGAAAAAGTCATGAATTATTTTTAAATATAAAGTCTTTAGACCGTCCTATTTGACTCAGATGATATTCAAATCCAAGTTTAGAGACC

Reverse complement sequence

GGTCTCTAAACTTGGATTTGAATATCATCTGAGTCAAATAGGACGGTCTAAAGACTTTATATTTAAAAATAATTCATGACTTTTTCATGTGAACTCTAAT[G/A]
AAGACAAACTTTGGGCCTGTTTGGGGAAGCTTTAGATTCTGAGAAGCAGTTGTTTGGTAGCCAGCTTCTGAGAATCTGGAAAAGCTCTAAAACCTAGCTT

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 77.90% 19.00% 3.07% 0.00% NA
All Indica  2759 63.30% 31.80% 4.89% 0.00% NA
All Japonica  1512 99.50% 0.30% 0.20% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 27.20% 62.40% 10.42% 0.00% NA
Indica II  465 40.40% 54.00% 5.59% 0.00% NA
Indica III  913 96.90% 2.10% 0.99% 0.00% NA
Indica Intermediate  786 65.00% 30.20% 4.83% 0.00% NA
Temperate Japonica  767 99.10% 0.50% 0.39% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 76.70% 16.70% 6.67% 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
vg0624609971 C -> T LOC_Os06g41140-LOC_Os06g41150 intergenic_region ; MODIFIER silent_mutation Average:29.007; most accessible tissue: Callus, score: 40.84 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624609971 NA 1.69E-11 mr1065_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
vg0624609971 NA 1.99E-10 mr1091_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
vg0624609971 NA 1.99E-08 mr1112_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
vg0624609971 NA 9.68E-11 mr1234_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
vg0624609971 NA 4.59E-06 mr1346_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
vg0624609971 NA 4.28E-08 mr1536_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
vg0624609971 NA 6.19E-10 mr1582_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
vg0624609971 NA 3.65E-08 mr1707_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