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Detailed information for vg0500853907:

Variant ID: vg0500853907 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 853907
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CACGGATCGGTGCCGCAGTTGCGTGTGTTCTAGAACTGGACCCTGCTTGCTACTAAATCGACTGTGCGGCACCAAATCTTCCGTTTGTCAGCGCGTCATA[C/T]
GTCGGCTGGATATTTGGTGTGTTCACAAGTTGATCTGTGCAGTGGATTGATTGTCTTGTCTCGTCTTGCAAATAAGCTCAACTAAGTTGAGACGCACTGA

Reverse complement sequence

TCAGTGCGTCTCAACTTAGTTGAGCTTATTTGCAAGACGAGACAAGACAATCAATCCACTGCACAGATCAACTTGTGAACACACCAAATATCCAGCCGAC[G/A]
TATGACGCGCTGACAAACGGAAGATTTGGTGCCGCACAGTCGATTTAGTAGCAAGCAGGGTCCAGTTCTAGAACACACGCAACTGCGGCACCGATCCGTG

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 88.20% 11.80% 0.00% 0.00% NA
All Indica  2759 89.20% 10.80% 0.00% 0.00% NA
All Japonica  1512 91.60% 8.40% 0.00% 0.00% NA
Aus  269 77.00% 23.00% 0.00% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 87.10% 12.90% 0.00% 0.00% NA
Indica III  913 86.70% 13.30% 0.00% 0.00% NA
Indica Intermediate  786 86.80% 13.20% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 78.40% 21.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 37.50% 62.50% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0500853907 C -> T LOC_Os05g02480.1 downstream_gene_variant ; 3494.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500853907 C -> T LOC_Os05g02500.1 downstream_gene_variant ; 4387.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500853907 C -> T LOC_Os05g02500.2 downstream_gene_variant ; 4387.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500853907 C -> T LOC_Os05g02500.3 downstream_gene_variant ; 4387.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500853907 C -> T LOC_Os05g02490.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500853907 4.69E-06 2.48E-08 mr1346 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
vg0500853907 NA 5.00E-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
vg0500853907 NA 4.74E-06 mr1754_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