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Detailed information for vg0112302656:

Variant ID: vg0112302656 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 12302656
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTCCATCATGACATCCAAAAGTTCACTCATTTTCTGCTGTTGAGATCATGTGTCTTCAACTAGGGCCCTGTTTTTAGATTCCAACTTTTTTCTTCAAA[C/T]
TTCTAACTTTTCCATCCCATCGAACTTTCCTACATACACAAACTTTCAACTTTTCCATCACATCGTTTCAATTTCTTCAAACTTTCAATTTTAACGTGGA

Reverse complement sequence

TCCACGTTAAAATTGAAAGTTTGAAGAAATTGAAACGATGTGATGGAAAAGTTGAAAGTTTGTGTATGTAGGAAAGTTCGATGGGATGGAAAAGTTAGAA[G/A]
TTTGAAGAAAAAAGTTGGAATCTAAAAACAGGGCCCTAGTTGAAGACACATGATCTCAACAGCAGAAAATGAGTGAACTTTTGGATGTCATGATGGAGTA

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 98.10% 1.90% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.30% 5.60% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 98.00% 1.80% 0.13% 0.00% NA
Tropical Japonica  504 94.00% 6.00% 0.00% 0.00% NA
Japonica Intermediate  241 83.00% 17.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0112302656 C -> T LOC_Os01g21920.1 upstream_gene_variant ; 4467.0bp to feature; MODIFIER silent_mutation Average:80.902; most accessible tissue: Minghui63 young leaf, score: 94.096 N N N N
vg0112302656 C -> T LOC_Os01g21930.1 upstream_gene_variant ; 2675.0bp to feature; MODIFIER silent_mutation Average:80.902; most accessible tissue: Minghui63 young leaf, score: 94.096 N N N N
vg0112302656 C -> T LOC_Os01g21940.1 downstream_gene_variant ; 514.0bp to feature; MODIFIER silent_mutation Average:80.902; most accessible tissue: Minghui63 young leaf, score: 94.096 N N N N
vg0112302656 C -> T LOC_Os01g21930-LOC_Os01g21940 intergenic_region ; MODIFIER silent_mutation Average:80.902; most accessible tissue: Minghui63 young leaf, score: 94.096 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)
vg0112302656 C T -0.01 0.0 0.0 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0112302656 1.42E-07 1.42E-07 mr1008 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
vg0112302656 5.60E-07 5.60E-07 mr1009 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
vg0112302656 NA 7.78E-07 mr1114 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
vg0112302656 NA 1.77E-07 mr1118 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
vg0112302656 NA 7.81E-06 mr1242 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
vg0112302656 2.16E-06 5.26E-07 mr1495 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
vg0112302656 NA 8.71E-06 mr1496 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
vg0112302656 5.58E-06 5.59E-06 mr1750 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
vg0112302656 NA 2.60E-06 mr1917 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