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Detailed information for vg0729015054:

Variant ID: vg0729015054 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 29015054
Reference Allele: GAAAlternative Allele: AAA,G
Primary Allele: GAASecondary Allele: AAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTTGTGTGGAGGTTGTCTCTTGATTTAGGGGTGGCTCATCATCTCTCTCTTTACTTTTCTCCTCCACCTCATCACCCAATATAATGTGGCACTTGTA[GAA/AAA,G]
GCAACATATGAAACATTATAGCACTTGCCCTAATGTATTGAATCATCCGAGACATGTGTATAGGAAGACGTATGGTATGGTGGTCAGTTGCGGGATGTCT

Reverse complement sequence

AGACATCCCGCAACTGACCACCATACCATACGTCTTCCTATACACATGTCTCGGATGATTCAATACATTAGGGCAAGTGCTATAATGTTTCATATGTTGC[TTC/TTT,C]
TACAAGTGCCACATTATATTGGGTGATGAGGTGGAGGAGAAAAGTAAAGAGAGAGATGATGAGCCACCCCTAAATCAAGAGACAACCTCCACACAAATTT

Allele Frequencies:

Populations Population SizeFrequency of GAA(primary allele) Frequency of AAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 1.10% 0.93% 0.51% G: 0.30%
All Indica  2759 99.80% 0.00% 0.00% 0.00% G: 0.18%
All Japonica  1512 92.10% 3.40% 2.84% 1.59% G: 0.07%
Aus  269 98.90% 0.00% 0.00% 0.00% G: 1.12%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.00% 0.00% 0.00% G: 0.33%
Indica Intermediate  786 99.60% 0.10% 0.00% 0.00% G: 0.25%
Temperate Japonica  767 92.30% 6.10% 1.56% 0.00% NA
Tropical Japonica  504 90.10% 0.00% 5.16% 4.76% NA
Japonica Intermediate  241 95.90% 1.70% 2.07% 0.00% G: 0.41%
VI/Aromatic  96 96.90% 0.00% 0.00% 0.00% G: 3.12%
Intermediate  90 95.60% 1.10% 1.11% 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
vg0729015054 GAA -> DEL N N silent_mutation Average:91.175; most accessible tissue: Callus, score: 98.504 N N N N
vg0729015054 GAA -> AAA LOC_Os07g48510.1 upstream_gene_variant ; 1802.0bp to feature; MODIFIER silent_mutation Average:91.175; most accessible tissue: Callus, score: 98.504 N N N N
vg0729015054 GAA -> AAA LOC_Os07g48510.2 upstream_gene_variant ; 1802.0bp to feature; MODIFIER silent_mutation Average:91.175; most accessible tissue: Callus, score: 98.504 N N N N
vg0729015054 GAA -> AAA LOC_Os07g48510-LOC_Os07g48520 intergenic_region ; MODIFIER silent_mutation Average:91.175; most accessible tissue: Callus, score: 98.504 N N N N
vg0729015054 GAA -> G LOC_Os07g48510.1 upstream_gene_variant ; 1803.0bp to feature; MODIFIER silent_mutation Average:91.175; most accessible tissue: Callus, score: 98.504 N N N N
vg0729015054 GAA -> G LOC_Os07g48510.2 upstream_gene_variant ; 1803.0bp to feature; MODIFIER silent_mutation Average:91.175; most accessible tissue: Callus, score: 98.504 N N N N
vg0729015054 GAA -> G LOC_Os07g48510-LOC_Os07g48520 intergenic_region ; MODIFIER silent_mutation Average:91.175; most accessible tissue: Callus, score: 98.504 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)
vg0729015054 GAA AAA -0.01 -0.01 0.0 -0.01 -0.01 -0.01
vg0729015054 GAA G 0.05 -0.03 -0.08 -0.03 -0.03 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729015054 NA 3.46E-06 mr1354 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
vg0729015054 7.96E-06 1.25E-08 mr1549 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
vg0729015054 3.97E-06 1.35E-10 mr1757 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
vg0729015054 4.14E-07 1.43E-11 mr1549_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
vg0729015054 NA 5.16E-07 mr1550_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
vg0729015054 5.94E-07 4.29E-11 mr1757_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