Search for Variation information by Variation ID:

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

Detailed information for vg0519469410:

Variant ID: vg0519469410 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19469410
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTACATATGTAGAACTATTATCCAATGGATAACTTTATCATTCTTAAGAAAGTATCAGAAGGACTATAGTATAAAACATAGTACTACTAAACAAATTAG[T/C]
ATAAAATCTAGTTACTTTCTCAATAAACTGTAAAATTTCTTATATCGAATACATATGCCATGTTTTAGAAGTATGAAGTAACAACACCATAATAAGTTGT

Reverse complement sequence

ACAACTTATTATGGTGTTGTTACTTCATACTTCTAAAACATGGCATATGTATTCGATATAAGAAATTTTACAGTTTATTGAGAAAGTAACTAGATTTTAT[A/G]
CTAATTTGTTTAGTAGTACTATGTTTTATACTATAGTCCTTCTGATACTTTCTTAAGAATGATAAAGTTATCCATTGGATAATAGTTCTACATATGTACC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.40% 7.60% 0.02% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 79.20% 20.80% 0.07% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.80% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 41.10% 58.90% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.40% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0519469410 T -> C LOC_Os05g33200.1 upstream_gene_variant ; 816.0bp to feature; MODIFIER silent_mutation Average:36.976; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0519469410 T -> C LOC_Os05g33190.1 downstream_gene_variant ; 1503.0bp to feature; MODIFIER silent_mutation Average:36.976; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0519469410 T -> C LOC_Os05g33190-LOC_Os05g33200 intergenic_region ; MODIFIER silent_mutation Average:36.976; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519469410 NA 9.14E-06 mr1125 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
vg0519469410 1.13E-07 NA mr1301 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
vg0519469410 3.79E-06 NA mr1410 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
vg0519469410 5.14E-07 NA mr1301_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
vg0519469410 2.53E-06 NA mr1410_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