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Detailed information for vg1005451839:

Variant ID: vg1005451839 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5451839
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


TGTAAATTGCGAAACGAATCTTTTAAGCAATTGTGCCATGATTTAACAACGTGATGCTACAGTATTTGCTAATGACAGATTATTTGGGCTTAATAAATTC[A/G]
CCTCGCAGTTTCTAGGCGGAATCTGTAATTTGTTTTGTTATTAGTCCATGTTTAATATTTCAAATATATATGTGTATATCCGATGTGACACGCCAAAATT

Reverse complement sequence

AATTTTGGCGTGTCACATCGGATATACACATATATATTTGAAATATTAAACATGGACTAATAACAAAACAAATTACAGATTCCGCCTAGAAACTGCGAGG[T/C]
GAATTTATTAAGCCCAAATAATCTGTCATTAGCAAATACTGTAGCATCACGTTGTTAAATCATGGCACAATTGCTTAAAAGATTCGTTTCGCAATTTACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.30% 33.30% 0.34% 0.00% NA
All Indica  2759 64.60% 35.10% 0.33% 0.00% NA
All Japonica  1512 63.80% 35.80% 0.33% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 92.10% 7.90% 0.00% 0.00% NA
Indica II  465 77.00% 22.40% 0.65% 0.00% NA
Indica III  913 37.50% 62.20% 0.33% 0.00% NA
Indica Intermediate  786 67.90% 31.70% 0.38% 0.00% NA
Temperate Japonica  767 74.60% 25.30% 0.13% 0.00% NA
Tropical Japonica  504 52.40% 47.40% 0.20% 0.00% NA
Japonica Intermediate  241 53.50% 45.20% 1.24% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 67.80% 30.00% 2.22% 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
vg1005451839 A -> G LOC_Os10g10030.1 upstream_gene_variant ; 2765.0bp to feature; MODIFIER silent_mutation Average:33.852; most accessible tissue: Minghui63 root, score: 67.149 N N N N
vg1005451839 A -> G LOC_Os10g10030-LOC_Os10g10040 intergenic_region ; MODIFIER silent_mutation Average:33.852; most accessible tissue: Minghui63 root, score: 67.149 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005451839 NA 9.48E-06 mr1120 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
vg1005451839 NA 9.50E-06 mr1386 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
vg1005451839 2.53E-06 NA mr1768 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
vg1005451839 4.62E-06 5.39E-09 mr1768 Jap_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
vg1005451839 3.15E-11 NA mr1768_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
vg1005451839 1.20E-07 2.42E-10 mr1768_2 Jap_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