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Detailed information for vg0105532662:

Variant ID: vg0105532662 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5532662
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


GCTTAGCATTAGTTTGATCTCCATAGGAAAATATCAAGCTTTTTGAAAAATACAAGGTTGCATGGATGGTTTGCACACTCCTTTTTACAGCTTGATAGTA[C/G]
CTAAAAGAAAACCCGCCAAATTCTGTCGTCATTGGGTCCACAAGAGTTGTCATTTGAATGGATTCATGTGAAACATGCTCATTTTTCTCCATGATATGTG

Reverse complement sequence

CACATATCATGGAGAAAAATGAGCATGTTTCACATGAATCCATTCAAATGACAACTCTTGTGGACCCAATGACGACAGAATTTGGCGGGTTTTCTTTTAG[G/C]
TACTATCAAGCTGTAAAAAGGAGTGTGCAAACCATCCATGCAACCTTGTATTTTTCAAAAAGCTTGATATTTTCCTATGGAGATCAAACTAATGCTAAGC

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 88.50% 11.40% 0.02% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 66.80% 33.20% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 42.90% 57.10% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0105532662 C -> G LOC_Os01g10460.1 intron_variant ; MODIFIER silent_mutation Average:29.036; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105532662 3.63E-06 1.32E-10 mr1002 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
vg0105532662 NA 5.70E-08 mr1002 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
vg0105532662 NA 3.52E-11 mr1002_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
vg0105532662 NA 6.31E-08 mr1002_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
vg0105532662 NA 5.96E-06 mr1840_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