Search for Variation information by Variation ID:

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

Detailed information for vg0334515770:

Variant ID: vg0334515770 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34515770
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGTGAGCCTCCATGCCTATTTACTGCGTATGCGTGACGCACGCCTGCGTATATAAATGGTACGGTCGATGGGTCTCGCATATCCTCCCTCTAAAAAAAA[C/A]
TCAATTTTTGGATTTTCGTGTCTAGCGTTTGAACGTCCGTATTATTTTTAAAAAATATTAAAAATAAGTCACACAAAAAATATTATCCATGTTTTATCAT

Reverse complement sequence

ATGATAAAACATGGATAATATTTTTTGTGTGACTTATTTTTAATATTTTTTAAAAATAATACGGACGTTCAAACGCTAGACACGAAAATCCAAAAATTGA[G/T]
TTTTTTTTAGAGGGAGGATATGCGAGACCCATCGACCGTACCATTTATATACGCAGGCGTGCGTCACGCATACGCAGTAAATAGGCATGGAGGCTCACTG

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 92.10% 7.70% 0.13% 0.00% NA
All Indica  2759 87.00% 12.80% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 97.00% 2.40% 0.67% 0.00% NA
Indica II  465 89.70% 10.30% 0.00% 0.00% NA
Indica III  913 84.70% 15.20% 0.11% 0.00% NA
Indica Intermediate  786 80.40% 19.50% 0.13% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0334515770 C -> A LOC_Os03g60720.1 upstream_gene_variant ; 4491.0bp to feature; MODIFIER silent_mutation Average:85.275; most accessible tissue: Minghui63 panicle, score: 98.805 N N N N
vg0334515770 C -> A LOC_Os03g60720-LOC_Os03g60730 intergenic_region ; MODIFIER silent_mutation Average:85.275; most accessible tissue: Minghui63 panicle, score: 98.805 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)
vg0334515770 C A 0.0 -0.01 -0.02 -0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334515770 NA 1.45E-06 mr1066 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
vg0334515770 NA 4.76E-06 mr1066 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
vg0334515770 4.86E-07 NA mr1568 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
vg0334515770 3.02E-06 3.02E-06 mr1568 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