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Detailed information for vg0605296250:

Variant ID: vg0605296250 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5296250
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, A: 0.12, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TCGTTGGCAATGTTAATGCGACCTTGAAACAGCAGCGTGGGCGGATGGCTGAAGCTTTAGAGGTCAAACTTGAATTTCAAAGCAGGCTAGTTGCTTTTAC[A/C]
GGCGAAAAAAGCATTCTGGTTGATCATCTCAACAATTGGGTCCATCATCTTGCACAACGAGCTTAGCTCTTGATTTAGCACCAAAGGAATTCAGGGATCG

Reverse complement sequence

CGATCCCTGAATTCCTTTGGTGCTAAATCAAGAGCTAAGCTCGTTGTGCAAGATGATGGACCCAATTGTTGAGATGATCAACCAGAATGCTTTTTTCGCC[T/G]
GTAAAAGCAACTAGCCTGCTTTGAAATTCAAGTTTGACCTCTAAAGCTTCAGCCATCCGCCCACGCTGCTGTTTCAAGGTCGCATTAACATTGCCAACGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.90% 13.10% 0.02% 0.00% NA
All Indica  2759 79.50% 20.50% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 65.90% 34.10% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 74.60% 25.40% 0.00% 0.00% NA
Indica Intermediate  786 83.60% 16.40% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 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
vg0605296250 A -> C LOC_Os06g10310.1 upstream_gene_variant ; 3886.0bp to feature; MODIFIER silent_mutation Average:43.946; most accessible tissue: Callus, score: 68.045 N N N N
vg0605296250 A -> C LOC_Os06g10290.1 downstream_gene_variant ; 2790.0bp to feature; MODIFIER silent_mutation Average:43.946; most accessible tissue: Callus, score: 68.045 N N N N
vg0605296250 A -> C LOC_Os06g10300.1 intron_variant ; MODIFIER silent_mutation Average:43.946; most accessible tissue: Callus, score: 68.045 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605296250 3.97E-23 5.26E-42 mr1201 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
vg0605296250 3.10E-21 1.36E-42 mr1201 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
vg0605296250 1.42E-18 1.20E-30 mr1219 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
vg0605296250 1.25E-17 9.89E-37 mr1219 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
vg0605296250 5.45E-20 2.11E-36 mr1274 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
vg0605296250 9.00E-22 4.74E-38 mr1274 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
vg0605296250 NA 1.62E-06 mr1662 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
vg0605296250 2.38E-21 1.76E-37 mr1201_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
vg0605296250 8.43E-20 4.88E-37 mr1201_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
vg0605296250 2.18E-17 3.52E-28 mr1219_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
vg0605296250 1.52E-17 1.38E-33 mr1219_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
vg0605296250 5.72E-16 5.60E-34 mr1274_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
vg0605296250 9.05E-18 5.78E-36 mr1274_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