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Detailed information for vg0507049696:

Variant ID: vg0507049696 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7049696
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AGTACCATTCGCTTCTGCCTAGTATATTAGTAAGAAATATTTAAATCTTCCAGCTTGTATGATAGACAAACAAATACACACGGGCTTACATTGTTCGTGC[T/C]
TAGTTTTTTTAGAGGAGATGTATCGATCAGTAAGCACTAAGAGCACCCGCAATGGTAAAGTAAGTTGCTCTCTATAACATATGTACATCTCAGCAATAGA

Reverse complement sequence

TCTATTGCTGAGATGTACATATGTTATAGAGAGCAACTTACTTTACCATTGCGGGTGCTCTTAGTGCTTACTGATCGATACATCTCCTCTAAAAAAACTA[A/G]
GCACGAACAATGTAAGCCCGTGTGTATTTGTTTGTCTATCATACAAGCTGGAAGATTTAAATATTTCTTACTAATATACTAGGCAGAAGCGAATGGTACT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.50% 13.20% 1.25% 0.00% NA
All Indica  2759 75.80% 22.20% 2.03% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 89.40% 6.20% 4.37% 0.00% NA
Indica II  465 79.60% 18.30% 2.15% 0.00% NA
Indica III  913 71.90% 27.60% 0.55% 0.00% NA
Indica Intermediate  786 67.70% 30.40% 1.91% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 1.11% 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
vg0507049696 T -> C LOC_Os05g12280.1 downstream_gene_variant ; 185.0bp to feature; MODIFIER silent_mutation Average:60.8; most accessible tissue: Minghui63 flag leaf, score: 81.312 N N N N
vg0507049696 T -> C LOC_Os05g12270-LOC_Os05g12280 intergenic_region ; MODIFIER silent_mutation Average:60.8; most accessible tissue: Minghui63 flag leaf, score: 81.312 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507049696 9.14E-08 2.51E-08 mr1593 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
vg0507049696 4.10E-07 3.66E-07 mr1593 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
vg0507049696 1.35E-06 NA mr1593_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
vg0507049696 4.92E-06 1.30E-07 mr1593_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