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Detailed information for vg0311959649:

Variant ID: vg0311959649 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 11959649
Reference Allele: GAAlternative Allele: G,GAA
Primary Allele: GASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGTGAGACGAGGCGATGAGAAGCTGCGCCTCCTTGGGGGTCCCCATTTATAGAAGGGATTTACTGCCCATTTGTTACTGATTTACTGCTTGGAGTGAAG[GA/G,GAA]
AAAAAAAAATCCCGGGTGAGACGAAACGCGTGGTGTGGTGTGGGGTGCCTCGTGTCCATGGCGTGTGGGGTCCAGACCGGAGGAACGTTCTGGATGCTGG

Reverse complement sequence

CCAGCATCCAGAACGTTCCTCCGGTCTGGACCCCACACGCCATGGACACGAGGCACCCCACACCACACCACGCGTTTCGTCTCACCCGGGATTTTTTTTT[TC/C,TTC]
CTTCACTCCAAGCAGTAAATCAGTAACAAATGGGCAGTAAATCCCTTCTATAAATGGGGACCCCCAAGGAGGCGCAGCTTCTCATCGCCTCGTCTCACGT

Allele Frequencies:

Populations Population SizeFrequency of GA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.20% 4.70% 0.02% 0.00% GAA: 0.08%
All Indica  2759 98.80% 1.20% 0.00% 0.00% GAA: 0.07%
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 37.20% 62.50% 0.37% 0.00% NA
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 98.50% 1.40% 0.00% 0.00% GAA: 0.11%
Indica Intermediate  786 97.50% 2.40% 0.00% 0.00% GAA: 0.13%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 0.00% 0.00% GAA: 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
vg0311959649 GA -> G LOC_Os03g21040.2 5_prime_UTR_variant ; 159.0bp to feature; MODIFIER silent_mutation Average:96.507; most accessible tissue: Zhenshan97 panicle, score: 99.846 N N N N
vg0311959649 GA -> G LOC_Os03g21050.1 upstream_gene_variant ; 2863.0bp to feature; MODIFIER silent_mutation Average:96.507; most accessible tissue: Zhenshan97 panicle, score: 99.846 N N N N
vg0311959649 GA -> G LOC_Os03g21040.3 upstream_gene_variant ; 85.0bp to feature; MODIFIER silent_mutation Average:96.507; most accessible tissue: Zhenshan97 panicle, score: 99.846 N N N N
vg0311959649 GA -> GAA LOC_Os03g21040.2 5_prime_UTR_variant ; 160.0bp to feature; MODIFIER silent_mutation Average:96.507; most accessible tissue: Zhenshan97 panicle, score: 99.846 N N N N
vg0311959649 GA -> GAA LOC_Os03g21050.1 upstream_gene_variant ; 2862.0bp to feature; MODIFIER silent_mutation Average:96.507; most accessible tissue: Zhenshan97 panicle, score: 99.846 N N N N
vg0311959649 GA -> GAA LOC_Os03g21040.3 upstream_gene_variant ; 86.0bp to feature; MODIFIER silent_mutation Average:96.507; most accessible tissue: Zhenshan97 panicle, score: 99.846 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)
vg0311959649 GA G -0.02 0.14 0.1 -0.04 0.01 0.01
vg0311959649 GA GAA -0.05 0.07 0.12 -0.09 -0.03 0.0