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Detailed information for vg1224009039:

Variant ID: vg1224009039 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24009039
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTAATGTTCAAACACCCCATACGATACCCTGTATAAGTACCCGACACATTAACTGGATCTAAACAACACATTAACTGCTTTTGCATTCTGCTGCTGCT[G/A]
CTGCTCTAGCATACACAGGCCTGTCAGAGGAGGAATCAACCAACGACAGCTTCAAGAACCAGGATCTGTTTGATGTTGTTGCGTCCTGTGTGAAACAAAC

Reverse complement sequence

GTTTGTTTCACACAGGACGCAACAACATCAAACAGATCCTGGTTCTTGAAGCTGTCGTTGGTTGATTCCTCCTCTGACAGGCCTGTGTATGCTAGAGCAG[C/T]
AGCAGCAGCAGAATGCAAAAGCAGTTAATGTGTTGTTTAGATCCAGTTAATGTGTCGGGTACTTATACAGGGTATCGTATGGGGTGTTTGAACATTAATA

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 98.20% 1.30% 0.49% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 94.50% 4.00% 1.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 97.00% 1.80% 1.17% 0.00% NA
Tropical Japonica  504 96.40% 3.00% 0.60% 0.00% NA
Japonica Intermediate  241 82.60% 13.30% 4.15% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1224009039 G -> A LOC_Os12g39040.1 upstream_gene_variant ; 4345.0bp to feature; MODIFIER silent_mutation Average:58.087; most accessible tissue: Zhenshan97 panicle, score: 79.071 N N N N
vg1224009039 G -> A LOC_Os12g39030.1 intron_variant ; MODIFIER silent_mutation Average:58.087; most accessible tissue: Zhenshan97 panicle, score: 79.071 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224009039 8.86E-07 8.08E-11 mr1693 Jap_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
vg1224009039 NA 2.97E-06 mr1117_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
vg1224009039 NA 1.43E-06 mr1119_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
vg1224009039 NA 6.29E-06 mr1120_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
vg1224009039 NA 1.74E-06 mr1242_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
vg1224009039 NA 3.61E-06 mr1247_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
vg1224009039 NA 6.99E-06 mr1496_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
vg1224009039 NA 8.31E-06 mr1691_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
vg1224009039 NA 1.02E-06 mr1861_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
vg1224009039 7.27E-06 5.38E-08 mr1865_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