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Detailed information for vg0719531114:

Variant ID: vg0719531114 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19531114
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTCGGGTGTCGTGATCCCCCTTAGCGGTGTTGTTGAGCTGCCACTCTCACTCTCCATGACAGGATTCTTCAGATGAAACCCCAATCCGGATGGACGGG[C/T]
GACGGTGGCGCCTAAGGCATCATGACCTCCTTATAGTGCGTTGTAGCTCTTCTCTATTTTTTAAGCCCTTCTCACTTATCCGCCTCATCCCGACTAAACC

Reverse complement sequence

GGTTTAGTCGGGATGAGGCGGATAAGTGAGAAGGGCTTAAAAAATAGAGAAGAGCTACAACGCACTATAAGGAGGTCATGATGCCTTAGGCGCCACCGTC[G/A]
CCCGTCCATCCGGATTGGGGTTTCATCTGAAGAATCCTGTCATGGAGAGTGAGAGTGGCAGCTCAACAACACCGCTAAGGGGGATCACGACACCCGAAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.40% 6.60% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 79.70% 20.20% 0.07% 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% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 66.00% 33.90% 0.13% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 83.00% 17.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0719531114 C -> T LOC_Os07g32710.1 upstream_gene_variant ; 2062.0bp to feature; MODIFIER silent_mutation Average:57.553; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0719531114 C -> T LOC_Os07g32690.1 downstream_gene_variant ; 4811.0bp to feature; MODIFIER silent_mutation Average:57.553; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0719531114 C -> T LOC_Os07g32700.1 downstream_gene_variant ; 752.0bp to feature; MODIFIER silent_mutation Average:57.553; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0719531114 C -> T LOC_Os07g32700-LOC_Os07g32710 intergenic_region ; MODIFIER silent_mutation Average:57.553; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719531114 1.55E-06 NA mr1648 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
vg0719531114 NA 1.55E-07 mr1648 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
vg0719531114 NA 7.18E-06 mr1697 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