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Detailed information for vg0505143979:

Variant ID: vg0505143979 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5143979
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


AGTAAATTTCAGAATACAACATATGTAGAAACCAGGGACGGAGCTACCGTTGTTGCACCGGGGTCCTAGGACACCGATGGCCGGAGCTAAATTCCACTTG[A/G]
TACCTATGGTGTAGTTGAATGTGACCCCGGCAAAATTGTTGATTTAAACCCAGCCCATCTGATCATCTTGTATGAGCACAACTACTAATTAAATCTTGGG

Reverse complement sequence

CCCAAGATTTAATTAGTAGTTGTGCTCATACAAGATGATCAGATGGGCTGGGTTTAAATCAACAATTTTGCCGGGGTCACATTCAACTACACCATAGGTA[T/C]
CAAGTGGAATTTAGCTCCGGCCATCGGTGTCCTAGGACCCCGGTGCAACAACGGTAGCTCCGTCCCTGGTTTCTACATATGTTGTATTCTGAAATTTACT

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 81.60% 4.60% 2.86% 10.96% NA
All Indica  2759 86.70% 7.80% 2.75% 2.72% NA
All Japonica  1512 88.10% 0.10% 0.66% 11.18% NA
Aus  269 15.60% 0.00% 15.61% 68.77% NA
Indica I  595 92.30% 3.00% 2.86% 1.85% NA
Indica II  465 85.80% 8.80% 4.73% 0.65% NA
Indica III  913 88.80% 8.50% 0.88% 1.75% NA
Indica Intermediate  786 80.70% 9.90% 3.69% 5.73% NA
Temperate Japonica  767 85.30% 0.10% 0.52% 14.08% NA
Tropical Japonica  504 89.70% 0.00% 0.99% 9.33% NA
Japonica Intermediate  241 93.80% 0.00% 0.41% 5.81% NA
VI/Aromatic  96 15.60% 0.00% 5.21% 79.17% NA
Intermediate  90 82.20% 1.10% 2.22% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0505143979 A -> DEL N N silent_mutation Average:53.361; most accessible tissue: Callus, score: 69.21 N N N N
vg0505143979 A -> G LOC_Os05g09200.1 upstream_gene_variant ; 694.0bp to feature; MODIFIER silent_mutation Average:53.361; most accessible tissue: Callus, score: 69.21 N N N N
vg0505143979 A -> G LOC_Os05g09200-LOC_Os05g09210 intergenic_region ; MODIFIER silent_mutation Average:53.361; most accessible tissue: Callus, score: 69.21 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505143979 1.10E-06 3.35E-11 mr1352 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
vg0505143979 5.47E-06 4.83E-08 mr1352 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
vg0505143979 1.23E-06 1.23E-06 mr1905 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