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Detailed information for vg0412597650:

Variant ID: vg0412597650 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12597650
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAGATGTATCCGAGGCATGTTGAACATGTTTGCCTTTCTTGAAAGCATAAAACCACCCCCCCTCCCCTTTCCCACCTCACATGTCCCACCTCTTCCCCA[C/T]
CCCATCCCCTTCTCCTCTCACTTCAGATCGACAAAGAGTTCTATATAGTAGAGAGAGATAGAGAGAAAGCTAGGGATATTGAGAGTCTGACATCTGAAAA

Reverse complement sequence

TTTTCAGATGTCAGACTCTCAATATCCCTAGCTTTCTCTCTATCTCTCTCTACTATATAGAACTCTTTGTCGATCTGAAGTGAGAGGAGAAGGGGATGGG[G/A]
TGGGGAAGAGGTGGGACATGTGAGGTGGGAAAGGGGAGGGGGGGTGGTTTTATGCTTTCAAGAAAGGCAAACATGTTCAACATGCCTCGGATACATCTAA

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 96.90% 2.50% 0.63% 0.00% NA
All Indica  2759 94.70% 4.20% 1.05% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.60% 8.20% 3.19% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 94.90% 3.80% 1.27% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg0412597650 C -> T LOC_Os04g22235.1 upstream_gene_variant ; 3555.0bp to feature; MODIFIER silent_mutation Average:59.953; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0412597650 C -> T LOC_Os04g22240.1 upstream_gene_variant ; 169.0bp to feature; MODIFIER silent_mutation Average:59.953; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0412597650 C -> T LOC_Os04g22235-LOC_Os04g22240 intergenic_region ; MODIFIER silent_mutation Average:59.953; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412597650 1.67E-08 2.62E-07 mr1946 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