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Detailed information for vg0611438317:

Variant ID: vg0611438317 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11438317
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.24, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


GATCGTTCATTTGCTAGCTTTTTTTTTTACGAAAAACAGCAGGAAAGACTGCTAGTTCTTTACATTACTTAGCTGTACAGTTTTTTTTTTCTCAAATACG[C/T]
TAAAGAGTTGTGTAATAGTTCATTAAGATAGGAGGGAAGCAAAAGCATCCCTCACCCTACAAACGTACAGGACTTACGTTTACAAGAAAAATAAAACAAA

Reverse complement sequence

TTTGTTTTATTTTTCTTGTAAACGTAAGTCCTGTACGTTTGTAGGGTGAGGGATGCTTTTGCTTCCCTCCTATCTTAATGAACTATTACACAACTCTTTA[G/A]
CGTATTTGAGAAAAAAAAAACTGTACAGCTAAGTAATGTAAAGAACTAGCAGTCTTTCCTGCTGTTTTTCGTAAAAAAAAAAGCTAGCAAATGAACGATC

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 37.80% 15.80% 0.70% 45.75% NA
All Indica  2759 4.20% 21.40% 0.91% 73.50% NA
All Japonica  1512 88.50% 8.80% 0.26% 2.45% NA
Aus  269 76.20% 0.00% 0.37% 23.42% NA
Indica I  595 7.40% 2.00% 1.01% 89.58% NA
Indica II  465 3.00% 6.20% 0.43% 90.32% NA
Indica III  913 1.20% 44.00% 0.44% 54.33% NA
Indica Intermediate  786 5.90% 18.80% 1.65% 73.66% NA
Temperate Japonica  767 95.80% 0.50% 0.39% 3.26% NA
Tropical Japonica  504 74.80% 24.20% 0.00% 0.99% NA
Japonica Intermediate  241 93.80% 2.90% 0.41% 2.90% NA
VI/Aromatic  96 84.40% 7.30% 0.00% 8.33% NA
Intermediate  90 51.10% 16.70% 3.33% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611438317 C -> T LOC_Os06g19960.1 upstream_gene_variant ; 835.0bp to feature; MODIFIER silent_mutation Average:22.888; most accessible tissue: Callus, score: 60.114 N N N N
vg0611438317 C -> T LOC_Os06g19950-LOC_Os06g19960 intergenic_region ; MODIFIER silent_mutation Average:22.888; most accessible tissue: Callus, score: 60.114 N N N N
vg0611438317 C -> DEL N N silent_mutation Average:22.888; most accessible tissue: Callus, score: 60.114 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611438317 NA 9.48E-09 mr1068 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
vg0611438317 NA 7.22E-07 mr1111 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
vg0611438317 NA 6.24E-06 mr1121 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
vg0611438317 NA 1.04E-07 mr1144 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
vg0611438317 NA 4.59E-09 mr1068_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
vg0611438317 9.22E-06 NA mr1087_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
vg0611438317 NA 6.35E-07 mr1096_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
vg0611438317 4.70E-06 9.72E-08 mr1111_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
vg0611438317 NA 1.78E-06 mr1121_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
vg0611438317 NA 5.46E-08 mr1144_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
vg0611438317 2.31E-07 NA mr1165_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
vg0611438317 NA 1.22E-08 mr1526_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
vg0611438317 1.87E-06 NA mr1971_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