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Detailed information for vg0622463338:

Variant ID: vg0622463338 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22463338
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACCCCTTGCCGCCCCACCAGAGGGCGGCAAGGGTTTTCCTACAAAAAACCCTCCCTCCGTCACTGCCCATTCCTCCCCCGTTTGCCACGTCAGCTTGCC[G/A]
CCCCATAGGTGGGCGGCAGGGTCTATTTTTGTAATTTTTTTAGCCGATAGATTATTTTTGTAAATATTTTAAAAAAAAATCTAAAACCGAAAAAAACTCT

Reverse complement sequence

AGAGTTTTTTTCGGTTTTAGATTTTTTTTTAAAATATTTACAAAAATAATCTATCGGCTAAAAAAATTACAAAAATAGACCCTGCCGCCCACCTATGGGG[C/T]
GGCAAGCTGACGTGGCAAACGGGGGAGGAATGGGCAGTGACGGAGGGAGGGTTTTTTGTAGGAAAACCCTTGCCGCCCTCTGGTGGGGCGGCAAGGGGTC

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 94.90% 5.10% 0.02% 0.00% NA
All Indica  2759 98.30% 1.70% 0.00% 0.00% NA
All Japonica  1512 88.30% 11.70% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.80% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 68.10% 31.90% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 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
vg0622463338 G -> A LOC_Os06g37970.1 upstream_gene_variant ; 711.0bp to feature; MODIFIER silent_mutation Average:87.343; most accessible tissue: Minghui63 young leaf, score: 93.766 N N N N
vg0622463338 G -> A LOC_Os06g37990.1 upstream_gene_variant ; 3140.0bp to feature; MODIFIER silent_mutation Average:87.343; most accessible tissue: Minghui63 young leaf, score: 93.766 N N N N
vg0622463338 G -> A LOC_Os06g37980.1 downstream_gene_variant ; 812.0bp to feature; MODIFIER silent_mutation Average:87.343; most accessible tissue: Minghui63 young leaf, score: 93.766 N N N N
vg0622463338 G -> A LOC_Os06g37970-LOC_Os06g37980 intergenic_region ; MODIFIER silent_mutation Average:87.343; most accessible tissue: Minghui63 young leaf, score: 93.766 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)
vg0622463338 G A 0.02 0.02 0.01 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622463338 8.26E-06 NA mr1070_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
vg0622463338 2.01E-06 7.84E-07 mr1082_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
vg0622463338 6.56E-07 3.86E-06 mr1083_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
vg0622463338 9.81E-06 NA mr1085_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
vg0622463338 NA 8.48E-06 mr1217_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
vg0622463338 NA 1.51E-06 mr1850_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