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Detailed information for vg0719446596:

Variant ID: vg0719446596 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19446596
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCCATTGACCGCGCTAGATTAATCCCGTGCCCATGGCCCTATGCCCTGATGGTAGTACTGTGACCCTGTTTGAAAGATGCCCTGATGGTAGTACTAGGG[C/T]
CCTGTTTGAAAGATTAGCCTAGGGTTAATTTTGAGAGCTAATGTTTAGTTATGAATTGGTAGGCTAAAGGGTGACATGTTTGGATCCATGAGTTAATTCA

Reverse complement sequence

TGAATTAACTCATGGATCCAAACATGTCACCCTTTAGCCTACCAATTCATAACTAAACATTAGCTCTCAAAATTAACCCTAGGCTAATCTTTCAAACAGG[G/A]
CCCTAGTACTACCATCAGGGCATCTTTCAAACAGGGTCACAGTACTACCATCAGGGCATAGGGCCATGGGCACGGGATTAATCTAGCGCGGTCAATGGAC

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 95.70% 4.30% 0.02% 0.00% NA
All Indica  2759 93.00% 7.00% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.40% 6.60% 0.00% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 93.50% 6.50% 0.00% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0719446596 C -> T LOC_Os07g32610.2 upstream_gene_variant ; 652.0bp to feature; MODIFIER silent_mutation Average:73.972; most accessible tissue: Callus, score: 93.634 N N N N
vg0719446596 C -> T LOC_Os07g32610.1 upstream_gene_variant ; 967.0bp to feature; MODIFIER silent_mutation Average:73.972; most accessible tissue: Callus, score: 93.634 N N N N
vg0719446596 C -> T LOC_Os07g32600.1 downstream_gene_variant ; 3820.0bp to feature; MODIFIER silent_mutation Average:73.972; most accessible tissue: Callus, score: 93.634 N N N N
vg0719446596 C -> T LOC_Os07g32610-LOC_Os07g32620 intergenic_region ; MODIFIER silent_mutation Average:73.972; most accessible tissue: Callus, score: 93.634 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0719446596 C T -0.01 0.0 -0.01 -0.03 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719446596 NA 2.56E-06 mr1086 Ind_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
vg0719446596 3.31E-07 4.92E-09 mr1088 Ind_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
vg0719446596 3.92E-06 NA mr1103 Ind_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
vg0719446596 NA 5.57E-06 mr1107 Ind_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
vg0719446596 5.85E-06 NA mr1139 Ind_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
vg0719446596 1.65E-06 2.20E-08 mr1224 Ind_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
vg0719446596 1.00E-08 1.83E-10 mr1225 Ind_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
vg0719446596 7.57E-06 1.90E-07 mr1246 Ind_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
vg0719446596 8.40E-07 1.39E-07 mr1404 Ind_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
vg0719446596 1.66E-06 1.40E-06 mr1620 Ind_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
vg0719446596 NA 2.68E-06 mr1914_2 Ind_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