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Detailed information for vg0601604412:

Variant ID: vg0601604412 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1604412
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGGTTGTGTTTAGTTCCCTCAAACTTCCGAAAACCAATTGCACAGTTTGCATGTAAATCGCGAGACTAATCTTTTGAGCCTAATTACGCCATGATTTGA[C/T]
AATATTGTGCTACAGTAAATATTTGCTAATGGTGGATTAATTAAGCTTAATAGATTTATCTCACAGTTTACCAACGGAATATGTAATTTATTTTGTTATT

Reverse complement sequence

AATAACAAAATAAATTACATATTCCGTTGGTAAACTGTGAGATAAATCTATTAAGCTTAATTAATCCACCATTAGCAAATATTTACTGTAGCACAATATT[G/A]
TCAAATCATGGCGTAATTAGGCTCAAAAGATTAGTCTCGCGATTTACATGCAAACTGTGCAATTGGTTTTCGGAAGTTTGAGGGAACTAAACACAACCTA

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 84.00% 15.90% 0.06% 0.00% NA
All Indica  2759 79.10% 20.80% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 44.20% 55.80% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 81.90% 18.10% 0.00% 0.00% NA
Indica III  913 65.90% 33.80% 0.22% 0.00% NA
Indica Intermediate  786 77.20% 22.60% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0601604412 C -> T LOC_Os06g03960.1 upstream_gene_variant ; 2632.0bp to feature; MODIFIER silent_mutation Average:47.363; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0601604412 C -> T LOC_Os06g03970.1 upstream_gene_variant ; 1048.0bp to feature; MODIFIER silent_mutation Average:47.363; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0601604412 C -> T LOC_Os06g03960-LOC_Os06g03970 intergenic_region ; MODIFIER silent_mutation Average:47.363; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601604412 3.39E-07 2.13E-09 mr1310 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
vg0601604412 NA 1.05E-06 mr1504 Ind_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
vg0601604412 NA 4.17E-06 mr1571 Ind_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
vg0601604412 6.84E-07 6.84E-07 mr1926 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
vg0601604412 NA 3.82E-08 mr1769_2 Ind_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
vg0601604412 NA 1.44E-06 mr1951_2 Ind_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