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Detailed information for vg0208783532:

Variant ID: vg0208783532 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 8783532
Reference Allele: GAlternative Allele: A,GGCGTTGACTAAGTCTTTGTCCAACA
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TCGACTCCTCTAACTATCAAAACCGGTGCAAACAATACCCCTCAGTGGTTTTGGAGGACGTGGCGCCTACATGGCGGTCTTGACTAAGTCTTTGTCCAAC[G/A,GGCGTTGACTAAGTCTTTGTCCAACA]
TGGCGCTTACGTGGCACTAGAATAAAACCAAAAATAAAAAATATGTGGGACCCATACGTCATTCACACGAAGAAGTACTGTGGAACCACTGACATGTGGG

Reverse complement sequence

CCCACATGTCAGTGGTTCCACAGTACTTCTTCGTGTGAATGACGTATGGGTCCCACATATTTTTTATTTTTGGTTTTATTCTAGTGCCACGTAAGCGCCA[C/T,TGTTGGACAAAGACTTAGTCAACGCC]
GTTGGACAAAGACTTAGTCAAGACCGCCATGTAGGCGCCACGTCCTCCAAAACCACTGAGGGGTATTGTTTGCACCGGTTTTGATAGTTAGAGGAGTCGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.50% 27.50% 0.04% 0.00% NA
All Indica  2759 55.70% 44.20% 0.07% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 81.40% 18.60% 0.00% 0.00% NA
Indica I  595 31.80% 68.10% 0.17% 0.00% NA
Indica II  465 60.90% 39.10% 0.00% 0.00% NA
Indica III  913 76.70% 23.30% 0.00% 0.00% NA
Indica Intermediate  786 46.40% 53.40% 0.13% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0208783532 G -> A LOC_Os02g15630.1 upstream_gene_variant ; 389.0bp to feature; MODIFIER silent_mutation Average:73.488; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0208783532 G -> A LOC_Os02g15620.1 downstream_gene_variant ; 1909.0bp to feature; MODIFIER silent_mutation Average:73.488; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0208783532 G -> A LOC_Os02g15620-LOC_Os02g15630 intergenic_region ; MODIFIER silent_mutation Average:73.488; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0208783532 G -> GGCGTTGACTAAGTCTTTGTCCAACA LOC_Os02g15630.1 upstream_gene_variant ; 388.0bp to feature; MODIFIER N Average:73.488; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0208783532 G -> GGCGTTGACTAAGTCTTTGTCCAACA LOC_Os02g15620.1 downstream_gene_variant ; 1910.0bp to feature; MODIFIER N Average:73.488; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0208783532 G -> GGCGTTGACTAAGTCTTTGTCCAACA LOC_Os02g15620-LOC_Os02g15630 intergenic_region ; MODIFIER N Average:73.488; most accessible tissue: Zhenshan97 panicle, score: 90.268 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)
vg0208783532 G A -0.09 -0.06 -0.04 -0.06 -0.05 -0.04
vg0208783532 G GGCGT* -0.38 -0.41 -0.33 -0.27 -0.34 -0.34

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208783532 3.56E-06 NA mr1002 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
vg0208783532 1.18E-06 2.54E-06 mr1002 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
vg0208783532 2.87E-06 NA mr1399 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