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Detailed information for vg0600544519:

Variant ID: vg0600544519 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 544519
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.02, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


CATAAATTGCAAAGTTGCTTCTCAGATAATTATGAGATTCAACCAAAATTTTGAATTCTGACCATCAATTATTTCTGATATGCTTAGTTTAAAAATAAAA[G/C]
AATTAACATATGTAGATTTGCCTCGAAAGTTACTACAATATCAGAAACTTATTATAATATAAAATTGATTGTTGGAATTTGATAAGTTTGACCGAATCTT

Reverse complement sequence

AAGATTCGGTCAAACTTATCAAATTCCAACAATCAATTTTATATTATAATAAGTTTCTGATATTGTAGTAACTTTCGAGGCAAATCTACATATGTTAATT[C/G]
TTTTATTTTTAAACTAAGCATATCAGAAATAATTGATGGTCAGAATTCAAAATTTTGGTTGAATCTCATAATTATCTGAGAAGCAACTTTGCAATTTATG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.70% 24.00% 0.32% 0.00% NA
All Indica  2759 63.20% 36.30% 0.51% 0.00% NA
All Japonica  1512 97.70% 2.30% 0.00% 0.00% NA
Aus  269 70.30% 29.70% 0.00% 0.00% NA
Indica I  595 57.60% 42.00% 0.34% 0.00% NA
Indica II  465 72.70% 26.70% 0.65% 0.00% NA
Indica III  913 62.00% 37.80% 0.22% 0.00% NA
Indica Intermediate  786 63.10% 36.00% 0.89% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg0600544519 G -> C LOC_Os06g01972.1 upstream_gene_variant ; 1985.0bp to feature; MODIFIER silent_mutation Average:40.315; most accessible tissue: Callus, score: 64.59 N N N N
vg0600544519 G -> C LOC_Os06g01966.1 intron_variant ; MODIFIER silent_mutation Average:40.315; most accessible tissue: Callus, score: 64.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0600544519 4.67E-06 NA mr1063 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
vg0600544519 4.61E-06 7.79E-07 mr1063 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
vg0600544519 NA 2.15E-06 mr1180 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
vg0600544519 NA 8.77E-06 mr1310 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
vg0600544519 NA 4.58E-06 mr1692 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
vg0600544519 NA 1.38E-06 mr1968 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