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Detailed information for vg1223515277:

Variant ID: vg1223515277 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23515277
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCTGCGGATGCGGCGGTGGCTGCGGGTACGTTCGATCTTCAGCTATTGATTCTGAATATGTTTGCTATGTATTTGTCAACATAAACTGTCATAAGCTTT[G/T]
ATGATTTTGATGTACTTTCCATCATAGAAGAATACTATGTTAGCCCCAATAGTTCTGCTTACAATTGATTTGAAGTTATATTCAGTTGAAGCCATCCATA

Reverse complement sequence

TATGGATGGCTTCAACTGAATATAACTTCAAATCAATTGTAAGCAGAACTATTGGGGCTAACATAGTATTCTTCTATGATGGAAAGTACATCAAAATCAT[C/A]
AAAGCTTATGACAGTTTATGTTGACAAATACATAGCAAACATATTCAGAATCAATAGCTGAAGATCGAACGTACCCGCAGCCACCGCCGCATCCGCAGGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(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 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 89.10% 10.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 94.10% 5.90% 0.00% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 61.80% 38.20% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1223515277 G -> T LOC_Os12g38310.1 upstream_gene_variant ; 1375.0bp to feature; MODIFIER silent_mutation Average:59.172; most accessible tissue: Minghui63 root, score: 88.829 N N N N
vg1223515277 G -> T LOC_Os12g38280.1 downstream_gene_variant ; 4696.0bp to feature; MODIFIER silent_mutation Average:59.172; most accessible tissue: Minghui63 root, score: 88.829 N N N N
vg1223515277 G -> T LOC_Os12g38290.1 downstream_gene_variant ; 1800.0bp to feature; MODIFIER silent_mutation Average:59.172; most accessible tissue: Minghui63 root, score: 88.829 N N N N
vg1223515277 G -> T LOC_Os12g38320.1 downstream_gene_variant ; 4691.0bp to feature; MODIFIER silent_mutation Average:59.172; most accessible tissue: Minghui63 root, score: 88.829 N N N N
vg1223515277 G -> T LOC_Os12g38300.1 intron_variant ; MODIFIER silent_mutation Average:59.172; most accessible tissue: Minghui63 root, score: 88.829 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223515277 NA 4.58E-07 mr1693 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
vg1223515277 NA 4.08E-06 mr1807 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