Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0100436915:

Variant ID: vg0100436915 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 436915
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCCCAACAAAACCATGTGGCTTCCTTGTTGCAGAAAATAAACTAACTCACCTTGTGAATCGTTGTGGACTCTTTGTTGCTTGCCACAAGTTGAGAAATC[C/T]
TGGGATTCATGATGAGAATCGGTTGAGAAGACTTGGTCATCTCAACCACCGACGCAGGGATCGCCACTGTGCGCGAATGGCTCCATGGAAGCCTCGCCGA

Reverse complement sequence

TCGGCGAGGCTTCCATGGAGCCATTCGCGCACAGTGGCGATCCCTGCGTCGGTGGTTGAGATGACCAAGTCTTCTCAACCGATTCTCATCATGAATCCCA[G/A]
GATTTCTCAACTTGTGGCAAGCAACAAAGAGTCCACAACGATTCACAAGGTGAGTTAGTTTATTTTCTGCAACAAGGAAGCCACATGGTTTTGTTGGGAA

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 95.20% 4.80% 0.00% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 39.00% 61.00% 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 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0100436915 C -> T LOC_Os01g01810.1 upstream_gene_variant ; 4163.0bp to feature; MODIFIER silent_mutation Average:72.82; most accessible tissue: Minghui63 flag leaf, score: 90.43 N N N N
vg0100436915 C -> T LOC_Os01g01830.1 upstream_gene_variant ; 698.0bp to feature; MODIFIER silent_mutation Average:72.82; most accessible tissue: Minghui63 flag leaf, score: 90.43 N N N N
vg0100436915 C -> T LOC_Os01g01810-LOC_Os01g01830 intergenic_region ; MODIFIER silent_mutation Average:72.82; most accessible tissue: Minghui63 flag leaf, score: 90.43 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)
vg0100436915 C T -0.03 -0.02 -0.03 -0.02 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0100436915 NA 4.70E-07 mr1415 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
vg0100436915 NA 4.70E-07 mr1567 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
vg0100436915 NA 3.34E-08 mr1570 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
vg0100436915 3.05E-06 NA mr1580 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
vg0100436915 NA 2.98E-09 mr1567_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
vg0100436915 NA 2.40E-18 mr1961_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