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Detailed information for vg0616489538:

Variant ID: vg0616489538 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 16489538
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCGGAAGGGGCTTCAGCTCTACAGGCGCAACTCCAAGCTTTCCTTCAGCAACTCAACCAACCCCACTACATTTCAAGTACAACCCCATCGGCTCACCC[A/G]
GTGGGGAATACAAGTCAAGGTGCGCCTAATTAGTTGCCACCGATTCAGCCAGGCTCGGGACCTTCGCCGTGGAGTAAAGGACAGCAGTTCGACTTCGGCA

Reverse complement sequence

TGCCGAAGTCGAACTGCTGTCCTTTACTCCACGGCGAAGGTCCCGAGCCTGGCTGAATCGGTGGCAACTAATTAGGCGCACCTTGACTTGTATTCCCCAC[T/C]
GGGTGAGCCGATGGGGTTGTACTTGAAATGTAGTGGGGTTGGTTGAGTTGCTGAAGGAAAGCTTGGAGTTGCGCCTGTAGAGCTGAAGCCCCTTCCGCCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.20% 0.10% 10.52% 29.09% NA
All Indica  2759 37.40% 0.20% 17.54% 44.80% NA
All Japonica  1512 92.90% 0.00% 0.40% 6.68% NA
Aus  269 96.30% 0.00% 0.37% 3.35% NA
Indica I  595 23.20% 0.00% 15.97% 60.84% NA
Indica II  465 37.40% 0.20% 15.70% 46.67% NA
Indica III  913 47.20% 0.10% 19.82% 32.86% NA
Indica Intermediate  786 36.90% 0.50% 17.18% 45.42% NA
Temperate Japonica  767 98.70% 0.00% 0.26% 1.04% NA
Tropical Japonica  504 83.50% 0.00% 0.60% 15.87% NA
Japonica Intermediate  241 94.20% 0.00% 0.41% 5.39% NA
VI/Aromatic  96 90.60% 0.00% 0.00% 9.38% NA
Intermediate  90 70.00% 1.10% 6.67% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0616489538 A -> G LOC_Os06g28910.1 upstream_gene_variant ; 1042.0bp to feature; MODIFIER silent_mutation Average:16.425; most accessible tissue: Minghui63 root, score: 23.574 N N N N
vg0616489538 A -> G LOC_Os06g28920.1 upstream_gene_variant ; 1979.0bp to feature; MODIFIER silent_mutation Average:16.425; most accessible tissue: Minghui63 root, score: 23.574 N N N N
vg0616489538 A -> G LOC_Os06g28890.1 downstream_gene_variant ; 4073.0bp to feature; MODIFIER silent_mutation Average:16.425; most accessible tissue: Minghui63 root, score: 23.574 N N N N
vg0616489538 A -> G LOC_Os06g28900.1 downstream_gene_variant ; 231.0bp to feature; MODIFIER silent_mutation Average:16.425; most accessible tissue: Minghui63 root, score: 23.574 N N N N
vg0616489538 A -> G LOC_Os06g28900-LOC_Os06g28910 intergenic_region ; MODIFIER silent_mutation Average:16.425; most accessible tissue: Minghui63 root, score: 23.574 N N N N
vg0616489538 A -> DEL N N silent_mutation Average:16.425; most accessible tissue: Minghui63 root, score: 23.574 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0616489538 NA 2.40E-06 mr1728 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
vg0616489538 5.62E-06 NA mr1544_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
vg0616489538 4.02E-06 NA mr1544_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