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Detailed information for vg0223029780:

Variant ID: vg0223029780 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 23029780
Reference Allele: GAAlternative Allele: AA,G
Primary Allele: GASecondary Allele: AA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGCGCCTGGAACACTGCATGTGTGGCGCTTTCCATCGACGATCTTCGATGGCGTATTGTGCGGGTATGATGGGTATGATGGGTTGCTGTGGGTTCAAGT[GA/AA,G]
AAAAACCTTGCTTGGCCTTATAGCAAGCTGTGCGCACCGGCGCCGGAGAGGTGTATGATCGACGAGCTCACCGAAGAATGGCACGTACATAAACAAGTTC

Reverse complement sequence

GAACTTGTTTATGTACGTGCCATTCTTCGGTGAGCTCGTCGATCATACACCTCTCCGGCGCCGGTGCGCACAGCTTGCTATAAGGCCAAGCAAGGTTTTT[TC/TT,C]
ACTTGAACCCACAGCAACCCATCATACCCATCATACCCGCACAATACGCCATCGAAGATCGTCGATGGAAAGCGCCACACATGCAGTGTTCCAGGCGCCC

Allele Frequencies:

Populations Population SizeFrequency of GA(primary allele) Frequency of AA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 3.10% 2.20% 0.00% G: 0.04%
All Indica  2759 90.90% 5.30% 3.73% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 77.50% 11.30% 11.26% 0.00% NA
Indica II  465 87.70% 9.20% 3.01% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 92.50% 4.70% 2.80% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 0.00% 0.00% G: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0223029780 GA -> G LOC_Os02g38100.1 upstream_gene_variant ; 4447.0bp to feature; MODIFIER silent_mutation Average:75.849; most accessible tissue: Callus, score: 89.594 N N N N
vg0223029780 GA -> G LOC_Os02g38090.1 downstream_gene_variant ; 3947.0bp to feature; MODIFIER silent_mutation Average:75.849; most accessible tissue: Callus, score: 89.594 N N N N
vg0223029780 GA -> G LOC_Os02g38090-LOC_Os02g38100 intergenic_region ; MODIFIER silent_mutation Average:75.849; most accessible tissue: Callus, score: 89.594 N N N N
vg0223029780 GA -> AA LOC_Os02g38100.1 upstream_gene_variant ; 4448.0bp to feature; MODIFIER silent_mutation Average:75.849; most accessible tissue: Callus, score: 89.594 N N N N
vg0223029780 GA -> AA LOC_Os02g38090.1 downstream_gene_variant ; 3946.0bp to feature; MODIFIER silent_mutation Average:75.849; most accessible tissue: Callus, score: 89.594 N N N N
vg0223029780 GA -> AA LOC_Os02g38090-LOC_Os02g38100 intergenic_region ; MODIFIER silent_mutation Average:75.849; most accessible tissue: Callus, score: 89.594 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)
vg0223029780 GA AA 0.01 -0.04 -0.03 -0.04 -0.08 -0.06
vg0223029780 GA G 0.14 0.07 0.05 0.11 0.12 0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223029780 7.67E-07 1.26E-12 mr1038 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
vg0223029780 3.85E-06 2.50E-12 mr1038 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
vg0223029780 8.50E-06 4.21E-06 mr1057 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
vg0223029780 NA 9.58E-07 mr1074 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
vg0223029780 NA 1.64E-08 mr1141 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
vg0223029780 NA 7.34E-06 mr1222 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
vg0223029780 1.25E-08 4.56E-17 mr1389 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
vg0223029780 3.61E-07 4.31E-15 mr1389 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
vg0223029780 2.63E-06 2.81E-14 mr1038_2 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
vg0223029780 8.42E-06 7.04E-13 mr1038_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
vg0223029780 5.42E-08 2.31E-09 mr1057_2 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
vg0223029780 NA 3.30E-07 mr1074_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
vg0223029780 NA 9.79E-06 mr1095_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
vg0223029780 NA 6.98E-10 mr1141_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
vg0223029780 NA 6.77E-06 mr1146_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
vg0223029780 NA 2.84E-06 mr1148_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
vg0223029780 5.96E-07 9.02E-15 mr1389_2 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
vg0223029780 9.12E-06 1.80E-13 mr1389_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
vg0223029780 NA 8.97E-06 mr1571_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