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Detailed information for vg0500210918:

Variant ID: vg0500210918 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 210918
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGACAGTCAAAGTTGGACACGGAAACTCGTGGTTTGTCTTTTTTGACGGAGGGAGTAGTCCATCCGTCCTCTAATATAACAAATTTTAACATTTCACTT[G/T]
AATTGTTTAATCATTCATCTTATTAAAAAAAATAGAATTATTATTTATTTTATTTGTGACTTACTTTATTATCAAAAGTACTTTAAACACAACTTTTCGT

Reverse complement sequence

ACGAAAAGTTGTGTTTAAAGTACTTTTGATAATAAAGTAAGTCACAAATAAAATAAATAATAATTCTATTTTTTTTAATAAGATGAATGATTAAACAATT[C/A]
AAGTGAAATGTTAAAATTTGTTATATTAGAGGACGGATGGACTACTCCCTCCGTCAAAAAAGACAAACCACGAGTTTCCGTGTCCAACTTTGACTGTCCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.60% 10.70% 0.44% 0.21% NA
All Indica  2759 86.80% 12.50% 0.36% 0.36% NA
All Japonica  1512 94.40% 5.00% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.40% 10.40% 0.17% 0.00% NA
Indica II  465 92.30% 7.50% 0.22% 0.00% NA
Indica III  913 76.80% 21.60% 0.66% 0.99% NA
Indica Intermediate  786 93.10% 6.50% 0.25% 0.13% NA
Temperate Japonica  767 95.60% 3.30% 1.17% 0.00% NA
Tropical Japonica  504 91.10% 8.70% 0.20% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 84.40% 1.04% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0500210918 G -> T LOC_Os05g01330.1 upstream_gene_variant ; 1225.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210918 G -> T LOC_Os05g01350.1 upstream_gene_variant ; 2649.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210918 G -> T LOC_Os05g01330-LOC_Os05g01350 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500210918 G -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0500210918 G T -0.02 -0.01 -0.01 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500210918 NA 1.46E-06 mr1382 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
vg0500210918 NA 3.09E-06 mr1057_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
vg0500210918 4.39E-06 NA mr1062_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
vg0500210918 NA 5.30E-06 mr1925_2 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