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Detailed information for vg0507079626:

Variant ID: vg0507079626 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7079626
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGGTGGTCCGCTCCGGGTGGAGGCTCCAAATATCTCATTTTTGGTTTCTCTGCTGCTTCATTCTGTGCTAGATCAGTTTGTCCTGGAAATTTATAGAT[C/A]
ACTGATGCTCTGTAAGATAATGTCATATTCCTCTTGATCACGGCTACCGTACAGAAGCAACAATTTCGATCACGGACAAAGCTTCCACGAACTGCAATGT

Reverse complement sequence

ACATTGCAGTTCGTGGAAGCTTTGTCCGTGATCGAAATTGTTGCTTCTGTACGGTAGCCGTGATCAAGAGGAATATGACATTATCTTACAGAGCATCAGT[G/T]
ATCTATAAATTTCCAGGACAAACTGATCTAGCACAGAATGAAGCAGCAGAGAAACCAAAAATGAGATATTTGGAGCCTCCACCCGGAGCGGACCACCAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.60% 4.40% 0.00% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 97.80% 2.20% 0.00% 0.00% NA
Aus  269 48.30% 51.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0507079626 C -> A LOC_Os05g12310.1 upstream_gene_variant ; 1268.0bp to feature; MODIFIER silent_mutation Average:57.444; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg0507079626 C -> A LOC_Os05g12320.1 upstream_gene_variant ; 3257.0bp to feature; MODIFIER silent_mutation Average:57.444; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg0507079626 C -> A LOC_Os05g12310-LOC_Os05g12320 intergenic_region ; MODIFIER silent_mutation Average:57.444; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507079626 NA 1.72E-07 mr1157 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
vg0507079626 NA 9.94E-06 mr1373 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
vg0507079626 NA 1.26E-08 mr1446 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
vg0507079626 NA 4.39E-07 mr1652 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
vg0507079626 NA 4.86E-06 mr1608_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
vg0507079626 2.07E-06 NA mr1613_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
vg0507079626 1.93E-07 NA mr1962_2 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