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Detailed information for vg1018126750:

Variant ID: vg1018126750 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 18126750
Reference Allele: GAAlternative Allele: TA,G
Primary Allele: GASecondary Allele: TA

Inferred Ancestral Allele : GA (evidence from allele frequency in Oryza rufipogon: GA: 0.72, G: 0.28, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


AACCTCAAATAAAGTCTATATTAGCCCCTCATCTATAAATATATAGATTAAAATTTTAGGGGGGTATTATGGAGGCTCTAATGGTATATTAGAGGGTAGG[GA/TA,G]
GGGTCTAAACACCCCCCGCCCCCATGGTGTCCCCGCCCCTGTCTACTCCTAATTTTCAGTTACGAAGAGATTCTTAATCTTTCGATGGCCTAAAGTTGAG

Reverse complement sequence

CTCAACTTTAGGCCATCGAAAGATTAAGAATCTCTTCGTAACTGAAAATTAGGAGTAGACAGGGGCGGGGACACCATGGGGGCGGGGGGTGTTTAGACCC[TC/TA,C]
CCTACCCTCTAATATACCATTAGAGCCTCCATAATACCCCCCTAAAATTTTAATCTATATATTTATAGATGAGGGGCTAATATAGACTTTATTTGAGGTT

Allele Frequencies:

Populations Population SizeFrequency of GA(primary allele) Frequency of TA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.10% 22.30% 0.55% 0.00% G: 0.08%
All Indica  2759 62.20% 36.90% 0.83% 0.00% G: 0.07%
All Japonica  1512 98.70% 1.20% 0.07% 0.00% NA
Aus  269 98.90% 0.40% 0.00% 0.00% G: 0.74%
Indica I  595 46.60% 52.60% 0.84% 0.00% NA
Indica II  465 76.60% 22.80% 0.65% 0.00% NA
Indica III  913 65.30% 34.00% 0.55% 0.00% G: 0.22%
Indica Intermediate  786 62.10% 36.60% 1.27% 0.00% NA
Temperate Japonica  767 99.20% 0.70% 0.13% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 80.00% 17.80% 2.22% 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
vg1018126750 GA -> G LOC_Os10g33990.1 downstream_gene_variant ; 2801.0bp to feature; MODIFIER silent_mutation Average:84.908; most accessible tissue: Zhenshan97 flower, score: 97.346 N N N N
vg1018126750 GA -> G LOC_Os10g33980-LOC_Os10g33990 intergenic_region ; MODIFIER silent_mutation Average:84.908; most accessible tissue: Zhenshan97 flower, score: 97.346 N N N N
vg1018126750 GA -> TA LOC_Os10g33990.1 downstream_gene_variant ; 2802.0bp to feature; MODIFIER silent_mutation Average:84.908; most accessible tissue: Zhenshan97 flower, score: 97.346 N N N N
vg1018126750 GA -> TA LOC_Os10g33980-LOC_Os10g33990 intergenic_region ; MODIFIER silent_mutation Average:84.908; most accessible tissue: Zhenshan97 flower, score: 97.346 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)
vg1018126750 GA G -0.13 -0.12 -0.08 -0.14 -0.12 -0.09
vg1018126750 GA TA 0.0 0.0 0.0 0.01 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018126750 5.63E-06 3.43E-08 mr1168 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
vg1018126750 NA 3.48E-06 mr1383 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
vg1018126750 NA 2.59E-06 mr1425 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
vg1018126750 NA 8.39E-06 mr1511 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
vg1018126750 NA 5.55E-06 mr1607 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
vg1018126750 5.76E-06 NA mr1817 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
vg1018126750 4.63E-06 4.15E-07 mr1817 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