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Detailed information for vg0106598597:

Variant ID: vg0106598597 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6598597
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGCGCCCACAGATTTGGCCCTCTTTTGTGGGATTCAGAGCCATGGACTGATGCATGATGAGAGAGAGCGATCAGAGAGAGGCCGGCCCCCGGCCGGCA[C/T]
AGCATGCATATGCAGCCTGCAGGTTTGGGGATTGATCAGGACCGGAATCGGATCACATGCATGTATAATGCTCTTGCTCGCTGGATGCCACCACCTCCAA

Reverse complement sequence

TTGGAGGTGGTGGCATCCAGCGAGCAAGAGCATTATACATGCATGTGATCCGATTCCGGTCCTGATCAATCCCCAAACCTGCAGGCTGCATATGCATGCT[G/A]
TGCCGGCCGGGGGCCGGCCTCTCTCTGATCGCTCTCTCTCATCATGCATCAGTCCATGGCTCTGAATCCCACAAAAGAGGGCCAAATCTGTGGGCGCGCC

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 77.20% 22.50% 0.21% 0.06% NA
All Indica  2759 80.60% 18.90% 0.36% 0.07% NA
All Japonica  1512 87.20% 12.70% 0.00% 0.07% NA
Aus  269 0.70% 99.30% 0.00% 0.00% NA
Indica I  595 88.20% 11.60% 0.17% 0.00% NA
Indica II  465 68.80% 29.00% 1.72% 0.43% NA
Indica III  913 92.10% 7.90% 0.00% 0.00% NA
Indica Intermediate  786 68.60% 31.30% 0.13% 0.00% NA
Temperate Japonica  767 99.10% 0.80% 0.00% 0.13% NA
Tropical Japonica  504 77.00% 23.00% 0.00% 0.00% NA
Japonica Intermediate  241 71.00% 29.00% 0.00% 0.00% NA
VI/Aromatic  96 30.20% 69.80% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0106598597 C -> T LOC_Os01g12110-LOC_Os01g12120 intergenic_region ; MODIFIER silent_mutation Average:78.986; most accessible tissue: Minghui63 panicle, score: 98.151 N N N N
vg0106598597 C -> DEL N N silent_mutation Average:78.986; most accessible tissue: Minghui63 panicle, score: 98.151 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)
vg0106598597 C T -0.02 -0.03 -0.04 -0.1 -0.06 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106598597 NA 5.76E-10 mr1207 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
vg0106598597 NA 3.04E-07 mr1574 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
vg0106598597 NA 4.20E-07 mr1644 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
vg0106598597 3.90E-06 3.90E-06 mr1050_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
vg0106598597 2.96E-06 2.58E-10 mr1310_2 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
vg0106598597 1.34E-06 NA mr1498_2 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
vg0106598597 NA 4.72E-07 mr1498_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
vg0106598597 7.01E-07 NA mr1769_2 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
vg0106598597 NA 2.21E-08 mr1769_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
vg0106598597 NA 8.32E-08 mr1924_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
vg0106598597 8.46E-07 NA mr1943_2 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
vg0106598597 1.88E-06 1.11E-10 mr1943_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