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Detailed information for vg0500535025:

Variant ID: vg0500535025 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 535025
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAACTTTATAATTATATAGCTTAACTAACAAGAGTTGATCCATTCACATCCATCGTACCCCTCCGTTTCATATTACAAGTTGTTTTAACCTTTTTCTA[G/T]
TATAATACCTTTAAGTTTGACTAATTTTATAAAATAATTAGCAACATCTACAATACCAAATTAGTTTTATTAAATATAATAACATTGAGTATATTTTGAT

Reverse complement sequence

ATCAAAATATACTCAATGTTATTATATTTAATAAAACTAATTTGGTATTGTAGATGTTGCTAATTATTTTATAAAATTAGTCAAACTTAAAGGTATTATA[C/A]
TAGAAAAAGGTTAAAACAACTTGTAATATGAAACGGAGGGGTACGATGGATGTGAATGGATCAACTCTTGTTAGTTAAGCTATATAATTATAAAGTTAAT

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 88.80% 11.00% 0.19% 0.00% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 67.30% 32.10% 0.60% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 89.40% 9.80% 0.78% 0.00% NA
Tropical Japonica  504 45.60% 54.20% 0.20% 0.00% NA
Japonica Intermediate  241 42.30% 56.80% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0500535025 G -> T LOC_Os05g01940.1 upstream_gene_variant ; 2821.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500535025 G -> T LOC_Os05g01920-LOC_Os05g01940 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500535025 1.11E-07 NA mr1057 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
vg0500535025 NA 8.34E-08 mr1248 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
vg0500535025 NA 1.40E-06 mr1338 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
vg0500535025 NA 8.52E-10 mr1563 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
vg0500535025 NA 6.49E-09 mr1851 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
vg0500535025 NA 1.04E-12 mr1864 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
vg0500535025 2.80E-06 NA mr1057_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
vg0500535025 9.04E-06 NA mr1563_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
vg0500535025 NA 1.14E-10 mr1563_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