Search for Variation information by Variation ID:

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

Detailed information for vg0630468525:

Variant ID: vg0630468525 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30468525
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGCCCAATGCGGTAAGTAATCTGGTTAATGATCTAGTAGTAGGCTTCGTTTGGAATATGATTACTACGTGTAACAACTTTTAGTTGGATGGAATGTATC[C/T]
CAATAATATAAATCTGGATATACCATGTCTAGATTTACAGTAATACGTTCCATCCAAGCAAAATTTACTATATTTTGATATGGAGGGAGTAGCTTTTTTA

Reverse complement sequence

TAAAAAAGCTACTCCCTCCATATCAAAATATAGTAAATTTTGCTTGGATGGAACGTATTACTGTAAATCTAGACATGGTATATCCAGATTTATATTATTG[G/A]
GATACATTCCATCCAACTAAAAGTTGTTACACGTAGTAATCATATTCCAAACGAAGCCTACTACTAGATCATTAACCAGATTACTTACCGCATTGGGCAT

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 84.50% 15.40% 0.11% 0.00% NA
All Indica  2759 97.40% 2.50% 0.11% 0.00% NA
All Japonica  1512 72.90% 27.00% 0.07% 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 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 95.50% 4.30% 0.22% 0.00% NA
Indica Intermediate  786 96.40% 3.40% 0.13% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 37.10% 62.70% 0.20% 0.00% NA
Japonica Intermediate  241 66.40% 33.60% 0.00% 0.00% NA
VI/Aromatic  96 25.00% 74.00% 1.04% 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
vg0630468525 C -> T LOC_Os06g50330.1 upstream_gene_variant ; 423.0bp to feature; MODIFIER silent_mutation Average:98.542; most accessible tissue: Callus, score: 99.908 N N N N
vg0630468525 C -> T LOC_Os06g50340.1 downstream_gene_variant ; 1520.0bp to feature; MODIFIER silent_mutation Average:98.542; most accessible tissue: Callus, score: 99.908 N N N N
vg0630468525 C -> T LOC_Os06g50330-LOC_Os06g50340 intergenic_region ; MODIFIER silent_mutation Average:98.542; most accessible tissue: Callus, score: 99.908 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)
vg0630468525 C T -0.01 0.0 0.0 -0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630468525 NA 2.78E-06 mr1138 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
vg0630468525 4.80E-06 1.18E-06 mr1159 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
vg0630468525 NA 3.91E-06 mr1064_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