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Detailed information for vg0132416907:

Variant ID: vg0132416907 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 32416907
Reference Allele: GAlternative Allele: A
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CTCAACCTAACCACTTGTTTACAAGAAGGTCGATGGTATTTCGCATCCAAAAGTATTGTGCAATACTTGCAGAGAAAAGCGGCTTACGAACGACAATGTC[G/A]
TGAACAACAGTGCGACTGGCGAGTGCTAACTATGGCACTCCCTCCATGGGAAGCCCGTCTAAGATGCAAGTGTGGTGATCGTTGTCAGGTTCTTCGTTCC

Reverse complement sequence

GGAACGAAGAACCTGACAACGATCACCACACTTGCATCTTAGACGGGCTTCCCATGGAGGGAGTGCCATAGTTAGCACTCGCCAGTCGCACTGTTGTTCA[C/T]
GACATTGTCGTTCGTAAGCCGCTTTTCTCTGCAAGTATTGCACAATACTTTTGGATGCGAAATACCATCGACCTTCTTGTAAACAAGTGGTTAGGTTGAG

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 51.20% 47.30% 1.48% 0.00% NA
All Indica  2759 25.10% 74.40% 0.47% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 23.80% 55.40% 20.82% 0.00% NA
Indica I  595 3.00% 97.00% 0.00% 0.00% NA
Indica II  465 6.50% 93.50% 0.00% 0.00% NA
Indica III  913 45.80% 53.80% 0.44% 0.00% NA
Indica Intermediate  786 28.80% 70.10% 1.15% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 73.30% 25.60% 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
vg0132416907 G -> A LOC_Os01g56280.1 missense_variant ; p.Arg295His; MODERATE nonsynonymous_codon ; R295H Average:34.955; most accessible tissue: Minghui63 young leaf, score: 53.016 unknown unknown DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0132416907 NA 1.01E-21 mr1155 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
vg0132416907 NA 3.23E-08 mr1213 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
vg0132416907 NA 6.05E-07 mr1237 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
vg0132416907 4.22E-06 4.22E-06 mr1340 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
vg0132416907 NA 5.40E-06 mr1667 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
vg0132416907 NA 3.70E-07 mr1915 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
vg0132416907 1.25E-06 1.25E-06 mr1972 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
vg0132416907 NA 2.50E-06 mr1133_2 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
vg0132416907 NA 4.44E-07 mr1212_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