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Detailed information for vg1227333750:

Variant ID: vg1227333750 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27333750
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCATTCTGCATTCTACCTGTGCTTGTGAGTAAAAATATTATATCGCGTGTGTGGCTAGATCAATAGCGATCAAGGCGGATGAAAAATGATCGAGAATTGA[C/T]
GGAAGTGTTAAAAATTAGAACGGATAACTACTAAAGTGAACCGGTATTTTTTGGTGCTATAAAAAAAACGTGAACTTTTAATGTTATATAACCAATTTTA

Reverse complement sequence

TAAAATTGGTTATATAACATTAAAAGTTCACGTTTTTTTTATAGCACCAAAAAATACCGGTTCACTTTAGTAGTTATCCGTTCTAATTTTTAACACTTCC[G/A]
TCAATTCTCGATCATTTTTCATCCGCCTTGATCGCTATTGATCTAGCCACACACGCGATATAATATTTTTACTCACAAGCACAGGTAGAATGCAGAATGC

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 93.50% 6.50% 0.00% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 93.70% 6.30% 0.00% 0.00% NA
Aus  269 38.30% 61.70% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 88.70% 11.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1227333750 C -> T LOC_Os12g44070.1 upstream_gene_variant ; 1671.0bp to feature; MODIFIER silent_mutation Average:53.538; most accessible tissue: Callus, score: 97.424 N N N N
vg1227333750 C -> T LOC_Os12g44080.1 downstream_gene_variant ; 2339.0bp to feature; MODIFIER silent_mutation Average:53.538; most accessible tissue: Callus, score: 97.424 N N N N
vg1227333750 C -> T LOC_Os12g44070-LOC_Os12g44080 intergenic_region ; MODIFIER silent_mutation Average:53.538; most accessible tissue: Callus, score: 97.424 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227333750 1.33E-06 NA mr1024_2 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
vg1227333750 2.43E-06 2.43E-06 mr1024_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
vg1227333750 NA 2.69E-09 mr1582_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