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Detailed information for vg1005366897:

Variant ID: vg1005366897 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5366897
Reference Allele: AAlternative Allele: G
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: 209. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGGTAACTGTCGACCAGAATGGTCAGAAAACACGTTGAGAGTTTGGACATCTTTTTAAATATTTTGTCACAGATGACCCCATGTATTCTGGATAAATC[A/G]
TAACATTTCTCACGGATTATAGCATTTGGTTAGTCTTACATTAACTGATGTAATAAATAGGCCGTAAAACTGAAGTTCTTTATTTCTTGGTGTGAATGGC

Reverse complement sequence

GCCATTCACACCAAGAAATAAAGAACTTCAGTTTTACGGCCTATTTATTACATCAGTTAATGTAAGACTAACCAAATGCTATAATCCGTGAGAAATGTTA[T/C]
GATTTATCCAGAATACATGGGGTCATCTGTGACAAAATATTTAAAAAGATGTCCAAACTCTCAACGTGTTTTCTGACCATTCTGGTCGACAGTTACCAAT

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 79.90% 20.10% 0.02% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 44.90% 55.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.50% 0.00% 0.00% NA
Temperate Japonica  767 27.90% 72.10% 0.00% 0.00% NA
Tropical Japonica  504 66.30% 33.70% 0.00% 0.00% NA
Japonica Intermediate  241 54.40% 45.60% 0.00% 0.00% NA
VI/Aromatic  96 47.90% 51.00% 1.04% 0.00% NA
Intermediate  90 63.30% 36.70% 0.00% 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
vg1005366897 A -> G LOC_Os10g09900.1 upstream_gene_variant ; 1691.0bp to feature; MODIFIER silent_mutation Average:34.546; most accessible tissue: Callus, score: 57.325 N N N N
vg1005366897 A -> G LOC_Os10g09920.1 upstream_gene_variant ; 2334.0bp to feature; MODIFIER silent_mutation Average:34.546; most accessible tissue: Callus, score: 57.325 N N N N
vg1005366897 A -> G LOC_Os10g09910.1 downstream_gene_variant ; 655.0bp to feature; MODIFIER silent_mutation Average:34.546; most accessible tissue: Callus, score: 57.325 N N N N
vg1005366897 A -> G LOC_Os10g09910-LOC_Os10g09920 intergenic_region ; MODIFIER silent_mutation Average:34.546; most accessible tissue: Callus, score: 57.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005366897 1.00E-14 6.37E-29 mr1768 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
vg1005366897 1.30E-06 5.80E-12 mr1768 Jap_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
vg1005366897 5.44E-21 2.14E-47 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
vg1005366897 7.50E-08 4.34E-13 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