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Detailed information for vg1207943829:

Variant ID: vg1207943829 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7943829
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTGGGACGAGGCTCATGTGTTGGGCAGTCGCGGAGCGCGGGTAAAGTGTACATCCACTGCAGTGTGAGTAAAACAAATCTATTCGAATAGCCGTGCTC[G/A]
CGGTTATTGAGCACCGGAACATGTATTACACTTGGGTAGACTCTAAATTCTTAACTTGTGTGGGATGGGTTATTGCATGATGATTTTTATGCTGTTGGAG

Reverse complement sequence

CTCCAACAGCATAAAAATCATCATGCAATAACCCATCCCACACAAGTTAAGAATTTAGAGTCTACCCAAGTGTAATACATGTTCCGGTGCTCAATAACCG[C/T]
GAGCACGGCTATTCGAATAGATTTGTTTTACTCACACTGCAGTGGATGTACACTTTACCCGCGCTCCGCGACTGCCCAACACATGAGCCTCGTCCCAACA

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 56.30% 17.00% 0.91% 25.77% NA
All Indica  2759 83.70% 3.00% 0.72% 12.61% NA
All Japonica  1512 6.10% 43.80% 0.93% 49.21% NA
Aus  269 67.70% 3.70% 1.49% 27.14% NA
Indica I  595 79.00% 3.70% 0.34% 16.97% NA
Indica II  465 88.80% 5.20% 0.43% 5.59% NA
Indica III  913 87.20% 0.70% 0.77% 11.39% NA
Indica Intermediate  786 80.20% 3.80% 1.15% 14.89% NA
Temperate Japonica  767 7.00% 68.60% 0.65% 23.73% NA
Tropical Japonica  504 5.80% 12.70% 1.59% 79.96% NA
Japonica Intermediate  241 3.70% 29.90% 0.41% 65.98% NA
VI/Aromatic  96 46.90% 21.90% 1.04% 30.21% NA
Intermediate  90 36.70% 32.20% 4.44% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1207943829 G -> DEL N N silent_mutation Average:65.036; most accessible tissue: Minghui63 flag leaf, score: 85.67 N N N N
vg1207943829 G -> A LOC_Os12g13980.1 upstream_gene_variant ; 1973.0bp to feature; MODIFIER silent_mutation Average:65.036; most accessible tissue: Minghui63 flag leaf, score: 85.67 N N N N
vg1207943829 G -> A LOC_Os12g13980-LOC_Os12g13990 intergenic_region ; MODIFIER silent_mutation Average:65.036; most accessible tissue: Minghui63 flag leaf, score: 85.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207943829 NA 2.40E-07 mr1041_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
vg1207943829 NA 2.60E-06 mr1289_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
vg1207943829 NA 4.43E-07 mr1293_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
vg1207943829 NA 5.61E-07 mr1302_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
vg1207943829 NA 2.46E-07 mr1418_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
vg1207943829 NA 3.05E-06 mr1420_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
vg1207943829 NA 7.22E-06 mr1467_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
vg1207943829 3.67E-06 NA mr1494_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
vg1207943829 NA 6.31E-06 mr1508_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
vg1207943829 NA 3.01E-09 mr1604_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
vg1207943829 NA 1.60E-08 mr1683_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
vg1207943829 NA 1.35E-08 mr1824_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
vg1207943829 NA 8.92E-14 mr1838_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