Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0134670870:

Variant ID: vg0134670870 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34670870
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAACTCGTGCATCTGAACCTTCTTTTATCATTTTAGTATTTGCTTACTGTATTTGCCTCCAATCATATGGGTGAGAGTTTGAGACATTTATAGGGGAAA[C/A]
TGTTTTAAACACTCGGGTAGACGTCCATCCGTTTCTTACATGTCATCTAAATAGTTATGAAAAATTTTCAAAAAAATTGACATGATAGGTTAATATGTAA

Reverse complement sequence

TTACATATTAACCTATCATGTCAATTTTTTTGAAAATTTTTCATAACTATTTAGATGACATGTAAGAAACGGATGGACGTCTACCCGAGTGTTTAAAACA[G/T]
TTTCCCCTATAAATGTCTCAAACTCTCACCCATATGATTGGAGGCAAATACAGTAAGCAAATACTAAAATGATAAAAGAAGGTTCAGATGCACGAGTTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.10% 9.00% 0.95% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 70.20% 27.00% 2.78% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 54.20% 40.90% 4.82% 0.00% NA
Tropical Japonica  504 93.70% 5.80% 0.60% 0.00% NA
Japonica Intermediate  241 72.20% 27.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 1.11% 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
vg0134670870 C -> A LOC_Os01g59970.1 downstream_gene_variant ; 3614.0bp to feature; MODIFIER silent_mutation Average:78.454; most accessible tissue: Zhenshan97 flag leaf, score: 90.631 N N N N
vg0134670870 C -> A LOC_Os01g59950-LOC_Os01g59970 intergenic_region ; MODIFIER silent_mutation Average:78.454; most accessible tissue: Zhenshan97 flag leaf, score: 90.631 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)
vg0134670870 C A -0.02 -0.02 -0.03 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134670870 NA 1.13E-06 mr1070 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
vg0134670870 NA 9.81E-07 mr1097 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
vg0134670870 NA 2.80E-07 mr1154 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
vg0134670870 NA 1.31E-06 mr1252 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
vg0134670870 3.05E-06 3.05E-06 mr1824 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
vg0134670870 NA 1.42E-06 mr1154_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
vg0134670870 NA 4.79E-06 mr1555_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
vg0134670870 3.87E-06 3.87E-06 mr1984_2 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