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Detailed information for vg0408983975:

Variant ID: vg0408983975 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 8983975
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCCCTTAAATAGGGGTTGGTCTTACCCTCTACAGGCCCTTCTCTACATCCAACTCGGGATAGAAACCAAAAGAAACCCGAAACATGCCTTCCCGAGTAA[G/T]
GAAACCCGAGACCCAACGAAAACAAACTCAGACTCGGACCCTGACGGTCTGACCGGCCCCATACCTGCGGTTAGACCGGCCCTACTAGCCGGTCAGACCG

Reverse complement sequence

CGGTCTGACCGGCTAGTAGGGCCGGTCTAACCGCAGGTATGGGGCCGGTCAGACCGTCAGGGTCCGAGTCTGAGTTTGTTTTCGTTGGGTCTCGGGTTTC[C/A]
TTACTCGGGAAGGCATGTTTCGGGTTTCTTTTGGTTTCTATCCCGAGTTGGATGTAGAGAAGGGCCTGTAGAGGGTAAGACCAACCCCTATTTAAGGGAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 2.20% 0.83% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 90.70% 6.80% 2.45% 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 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 84.00% 12.00% 4.04% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 1.20% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0408983975 G -> T LOC_Os04g16520.1 downstream_gene_variant ; 2544.0bp to feature; MODIFIER silent_mutation Average:49.159; most accessible tissue: Minghui63 flag leaf, score: 67.099 N N N N
vg0408983975 G -> T LOC_Os04g16530.1 intron_variant ; MODIFIER silent_mutation Average:49.159; most accessible tissue: Minghui63 flag leaf, score: 67.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0408983975 4.41E-07 3.78E-09 mr1035 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
vg0408983975 NA 1.66E-10 mr1062 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
vg0408983975 1.76E-06 5.10E-08 mr1626 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
vg0408983975 NA 5.58E-06 mr1035_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
vg0408983975 9.21E-06 5.57E-09 mr1062_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
vg0408983975 7.68E-06 2.38E-10 mr1631_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