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Detailed information for vg0215878891:

Variant ID: vg0215878891 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 15878891
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGCTGTAGATCAATGACAACAGTTGTTGGTGGAGTCGTCGGTGGTGCTTGGCATTGGTGCTAGATGTTGTCAGAGATACGAAGAAGCCCAGGAGGTCA[G/A]
GGTCGCGGCGGTGTGCGCGTCCTGCGTCGAAGCCGAGCCGGCGACGGAGATCAGGGCGATGCCGAGAAGGAGCTGGCTAGGGTTTTAGCTAGGTCGTGCA

Reverse complement sequence

TGCACGACCTAGCTAAAACCCTAGCCAGCTCCTTCTCGGCATCGCCCTGATCTCCGTCGCCGGCTCGGCTTCGACGCAGGACGCGCACACCGCCGCGACC[C/T]
TGACCTCCTGGGCTTCTTCGTATCTCTGACAACATCTAGCACCAATGCCAAGCACCACCGACGACTCCACCAACAACTGTTGTCATTGATCTACAGCCCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.60% 0.10% 0.08% 1.16% NA
All Indica  2759 99.90% 0.00% 0.00% 0.07% NA
All Japonica  1512 96.70% 0.10% 0.07% 3.11% NA
Aus  269 98.10% 0.70% 1.12% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.00% 0.13% NA
Temperate Japonica  767 98.20% 0.10% 0.13% 1.56% NA
Tropical Japonica  504 98.40% 0.00% 0.00% 1.59% NA
Japonica Intermediate  241 88.40% 0.40% 0.00% 11.20% NA
VI/Aromatic  96 94.80% 0.00% 0.00% 5.21% NA
Intermediate  90 98.90% 0.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0215878891 G -> A LOC_Os02g27010.1 upstream_gene_variant ; 960.0bp to feature; MODIFIER silent_mutation Average:61.946; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg0215878891 G -> A LOC_Os02g27000.1 downstream_gene_variant ; 2402.0bp to feature; MODIFIER silent_mutation Average:61.946; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg0215878891 G -> A LOC_Os02g27020.1 downstream_gene_variant ; 4436.0bp to feature; MODIFIER silent_mutation Average:61.946; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg0215878891 G -> A LOC_Os02g27000-LOC_Os02g27010 intergenic_region ; MODIFIER silent_mutation Average:61.946; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N
vg0215878891 G -> DEL N N silent_mutation Average:61.946; most accessible tissue: Minghui63 young leaf, score: 78.054 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0215878891 3.74E-06 4.78E-07 mr1129_2 Jap_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
vg0215878891 NA 1.37E-06 mr1257_2 Jap_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
vg0215878891 NA 6.45E-07 mr1865_2 Jap_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