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Detailed information for vg1002814950:

Variant ID: vg1002814950 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2814950
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


ACATATCACTTAAATGGTTATGATAACATGTATTATCATGTGATATATCACTCCATAAATATAGAGTAAAATACAGTAGCGGCCCTTAAACTTGCGGGCG[G/A]
ATGTCATCCAGGTCCACTAACTTGCAAATCGTGTAATTAGGCCACTAAACTTGCTAAATGTACCATCGCCGGTCCAAAATGCCGTTTGACCGCAGTCGCG

Reverse complement sequence

CGCGACTGCGGTCAAACGGCATTTTGGACCGGCGATGGTACATTTAGCAAGTTTAGTGGCCTAATTACACGATTTGCAAGTTAGTGGACCTGGATGACAT[C/T]
CGCCCGCAAGTTTAAGGGCCGCTACTGTATTTTACTCTATATTTATGGAGTGATATATCACATGATAATACATGTTATCATAACCATTTAAGTGATATGT

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 83.60% 12.10% 4.30% 0.00% NA
All Indica  2759 74.30% 20.70% 5.04% 0.00% NA
All Japonica  1512 95.80% 0.10% 4.03% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 55.00% 31.10% 13.95% 0.00% NA
Indica II  465 81.90% 14.00% 4.09% 0.00% NA
Indica III  913 77.70% 21.70% 0.66% 0.00% NA
Indica Intermediate  786 80.50% 15.50% 3.94% 0.00% NA
Temperate Japonica  767 91.90% 0.10% 7.95% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 2.20% 3.33% 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
vg1002814950 G -> A LOC_Os10g05630.1 upstream_gene_variant ; 1117.0bp to feature; MODIFIER silent_mutation Average:52.589; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg1002814950 G -> A LOC_Os10g05650.1 downstream_gene_variant ; 1394.0bp to feature; MODIFIER silent_mutation Average:52.589; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg1002814950 G -> A LOC_Os10g05630-LOC_Os10g05650 intergenic_region ; MODIFIER silent_mutation Average:52.589; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002814950 NA 8.01E-11 mr1403 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
vg1002814950 NA 7.55E-09 mr1403 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
vg1002814950 NA 6.26E-06 mr1547 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
vg1002814950 NA 1.03E-09 mr1709_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