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Detailed information for vg0412992801:

Variant ID: vg0412992801 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12992801
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAAAAATCATGAGCTGCAATTAAGAGTCCGATCATCTTAAGTTAGTATGTGAGTTTTTTTTAAGAAATATATTATACGACTCCTTCCGTATTTCCAAAA[G/A]
CGAACGGGCTTAAAACCCGACTCAAATACGGATCTATATTTTCAAAATAAAATGAACTTAAAAACCAACTCTATATATAGATGACATACCAAAGCAAAAA

Reverse complement sequence

TTTTTGCTTTGGTATGTCATCTATATATAGAGTTGGTTTTTAAGTTCATTTTATTTTGAAAATATAGATCCGTATTTGAGTCGGGTTTTAAGCCCGTTCG[C/T]
TTTTGGAAATACGGAAGGAGTCGTATAATATATTTCTTAAAAAAAACTCACATACTAACTTAAGATGATCGGACTCTTAATTGCAGCTCATGATTTTTTA

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 78.80% 21.20% 0.02% 0.00% NA
All Indica  2759 74.20% 25.70% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 0.70% 99.30% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 89.50% 10.50% 0.00% 0.00% NA
Indica III  913 50.20% 49.70% 0.11% 0.00% NA
Indica Intermediate  786 74.00% 26.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0412992801 G -> A LOC_Os04g22900.2 3_prime_UTR_variant ; 216.0bp to feature; MODIFIER silent_mutation Average:38.729; most accessible tissue: Callus, score: 60.091 N N N N
vg0412992801 G -> A LOC_Os04g22910.1 downstream_gene_variant ; 4877.0bp to feature; MODIFIER silent_mutation Average:38.729; most accessible tissue: Callus, score: 60.091 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412992801 NA 4.15E-06 mr1006 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
vg0412992801 NA 5.98E-06 mr1052 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
vg0412992801 NA 8.39E-07 mr1735 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
vg0412992801 8.99E-06 NA mr1705_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
vg0412992801 2.38E-07 5.06E-11 mr1705_2 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
vg0412992801 NA 2.03E-06 mr1762_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
vg0412992801 NA 2.35E-06 mr1929_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