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Detailed information for vg0716934852:

Variant ID: vg0716934852 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16934852
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAATAAATAATATTTACATAATATTTTTAATAAGACGAATAGTTAAACGGTATAAAAAATTCGGTGACACGAAGGGAGTAATATATATGGTTCATCGC[C/T]
AGTGATCGAGCGATGCACGCACTGATGATCTGATCATATACGTGTTGCATTCACACGCAGGTGAAGACGAGCAGCAGCGGCGGTGGCGGGAAGGAGGGGA

Reverse complement sequence

TCCCCTCCTTCCCGCCACCGCCGCTGCTGCTCGTCTTCACCTGCGTGTGAATGCAACACGTATATGATCAGATCATCAGTGCGTGCATCGCTCGATCACT[G/A]
GCGATGAACCATATATATTACTCCCTTCGTGTCACCGAATTTTTTATACCGTTTAACTATTCGTCTTATTAAAAATATTATGTAAATATTATTTATTTTG

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 79.10% 17.80% 3.15% 0.00% NA
All Indica  2759 97.70% 2.10% 0.18% 0.00% NA
All Japonica  1512 48.40% 42.50% 9.06% 0.00% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 99.00% 0.80% 0.22% 0.00% NA
Indica Intermediate  786 94.10% 5.60% 0.25% 0.00% NA
Temperate Japonica  767 68.70% 22.40% 8.87% 0.00% NA
Tropical Japonica  504 27.20% 65.70% 7.14% 0.00% NA
Japonica Intermediate  241 28.20% 58.10% 13.69% 0.00% NA
VI/Aromatic  96 7.30% 89.60% 3.12% 0.00% NA
Intermediate  90 71.10% 24.40% 4.44% 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
vg0716934852 C -> T LOC_Os07g28880.1 upstream_gene_variant ; 2219.0bp to feature; MODIFIER silent_mutation Average:59.815; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0716934852 C -> T LOC_Os07g28890.1 intron_variant ; MODIFIER silent_mutation Average:59.815; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716934852 2.44E-10 NA mr1238 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
vg0716934852 2.39E-09 NA mr1309 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
vg0716934852 NA 7.71E-06 mr1398 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
vg0716934852 4.20E-06 NA mr1484 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
vg0716934852 NA 9.12E-09 mr1554 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
vg0716934852 NA 6.09E-06 mr1602 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
vg0716934852 1.17E-07 NA mr1841 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
vg0716934852 8.59E-08 4.55E-15 mr1900 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
vg0716934852 NA 1.44E-07 mr1900 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