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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1218172024:

Variant ID: vg1218172024 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18172024
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: 0.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGCCAAGTTGTACGAAATCAACTGCAACTACGCATATACCCAACTCCTTAAAGTTTCTTGATCACAAGAAAAAAAAAACTTAAGAGGACATCGATGAG[G/C]
GTAACCTTAACCACCAGCATGACCACAACAGCACCATTCTAATGGGCAACGTCTGTGTTGGCACAACCTGTAGTTTGTCGAAGAACGGCCTTCTTTGCGC

Reverse complement sequence

GCGCAAAGAAGGCCGTTCTTCGACAAACTACAGGTTGTGCCAACACAGACGTTGCCCATTAGAATGGTGCTGTTGTGGTCATGCTGGTGGTTAAGGTTAC[C/G]
CTCATCGATGTCCTCTTAAGTTTTTTTTTTCTTGTGATCAAGAAACTTTAAGGAGTTGGGTATATGCGTAGTTGCAGTTGATTTCGTACAACTTGGCTGG

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 56.70% 24.50% 0.63% 18.15% NA
All Indica  2759 60.40% 37.70% 0.40% 1.52% NA
All Japonica  1512 50.50% 0.70% 0.53% 48.28% NA
Aus  269 61.70% 30.90% 1.49% 5.95% NA
Indica I  595 90.10% 7.70% 0.67% 1.51% NA
Indica II  465 51.60% 47.50% 0.43% 0.43% NA
Indica III  913 49.80% 49.40% 0.11% 0.66% NA
Indica Intermediate  786 55.30% 41.00% 0.51% 3.18% NA
Temperate Japonica  767 64.10% 0.80% 0.52% 34.55% NA
Tropical Japonica  504 27.80% 0.60% 0.79% 70.83% NA
Japonica Intermediate  241 54.80% 0.40% 0.00% 44.81% NA
VI/Aromatic  96 30.20% 8.30% 4.17% 57.29% NA
Intermediate  90 63.30% 16.70% 3.33% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218172024 G -> C LOC_Os12g30290.1 upstream_gene_variant ; 2980.0bp to feature; MODIFIER silent_mutation Average:64.812; most accessible tissue: Callus, score: 84.932 N N N N
vg1218172024 G -> C LOC_Os12g30290-LOC_Os12g30310 intergenic_region ; MODIFIER silent_mutation Average:64.812; most accessible tissue: Callus, score: 84.932 N N N N
vg1218172024 G -> DEL N N silent_mutation Average:64.812; most accessible tissue: Callus, score: 84.932 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218172024 NA 5.31E-06 mr1035 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
vg1218172024 NA 2.40E-06 mr1170 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
vg1218172024 NA 5.21E-07 mr1324 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
vg1218172024 NA 6.13E-07 mr1335 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
vg1218172024 NA 3.58E-06 mr1425 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
vg1218172024 NA 2.17E-06 mr1446 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
vg1218172024 NA 5.90E-08 mr1458 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
vg1218172024 6.37E-06 5.17E-09 mr1577 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
vg1218172024 NA 5.00E-07 mr1577 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
vg1218172024 NA 7.14E-06 mr1626 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
vg1218172024 NA 3.37E-06 mr1686 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
vg1218172024 NA 2.47E-06 mr1761 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