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Detailed information for vg0605311849:

Variant ID: vg0605311849 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5311849
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTAGCTCGATCACGATGGCAATATGGTCACAATTTTGAATGTAGAGGCTGTGTTTAGTGCTCTTCAAACCTTCATAAATTCCTTCACCTCAAGTGTTT[G/A]
GACATGCATGTAGTATTAAATGTAGAAAAAAAAACTAATTGGACAGTTTGTATGTAAATTGCGAGACGAATCTTTTGAGCCTAATTATACCATGATTTGA

Reverse complement sequence

TCAAATCATGGTATAATTAGGCTCAAAAGATTCGTCTCGCAATTTACATACAAACTGTCCAATTAGTTTTTTTTTCTACATTTAATACTACATGCATGTC[C/T]
AAACACTTGAGGTGAAGGAATTTATGAAGGTTTGAAGAGCACTAAACACAGCCTCTACATTCAAAATTGTGACCATATTGCCATCGTGATCGAGCTAGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.70% 41.80% 1.52% 0.00% NA
All Indica  2759 28.80% 69.20% 1.99% 0.00% NA
All Japonica  1512 97.60% 1.70% 0.73% 0.00% NA
Aus  269 95.20% 4.50% 0.37% 0.00% NA
Indica I  595 38.20% 58.00% 3.87% 0.00% NA
Indica II  465 5.20% 92.50% 2.37% 0.00% NA
Indica III  913 35.20% 64.50% 0.33% 0.00% NA
Indica Intermediate  786 28.20% 69.50% 2.29% 0.00% NA
Temperate Japonica  767 98.30% 1.00% 0.65% 0.00% NA
Tropical Japonica  504 97.00% 2.40% 0.60% 0.00% NA
Japonica Intermediate  241 96.30% 2.50% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 64.40% 30.00% 5.56% 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
vg0605311849 G -> A LOC_Os06g10350.1 upstream_gene_variant ; 3329.0bp to feature; MODIFIER silent_mutation Average:68.935; most accessible tissue: Minghui63 flower, score: 86.854 N N N N
vg0605311849 G -> A LOC_Os06g10330.1 downstream_gene_variant ; 4102.0bp to feature; MODIFIER silent_mutation Average:68.935; most accessible tissue: Minghui63 flower, score: 86.854 N N N N
vg0605311849 G -> A LOC_Os06g10340.1 downstream_gene_variant ; 1247.0bp to feature; MODIFIER silent_mutation Average:68.935; most accessible tissue: Minghui63 flower, score: 86.854 N N N N
vg0605311849 G -> A LOC_Os06g10340-LOC_Os06g10350 intergenic_region ; MODIFIER silent_mutation Average:68.935; most accessible tissue: Minghui63 flower, score: 86.854 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605311849 1.84E-22 1.83E-15 mr1201 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
vg0605311849 5.30E-27 1.35E-49 mr1201 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
vg0605311849 2.69E-18 2.58E-13 mr1219 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
vg0605311849 3.06E-23 1.41E-41 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
vg0605311849 2.86E-21 7.29E-10 mr1274 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
vg0605311849 1.64E-26 2.88E-43 mr1274 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
vg0605311849 1.22E-20 3.42E-13 mr1201_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
vg0605311849 1.04E-25 4.09E-42 mr1201_2 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
vg0605311849 8.99E-18 6.49E-14 mr1219_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
vg0605311849 1.02E-22 1.77E-38 mr1219_2 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
vg0605311849 8.16E-21 7.71E-12 mr1274_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
vg0605311849 1.68E-25 9.52E-41 mr1274_2 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