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Detailed information for vg0137335979:

Variant ID: vg0137335979 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 37335979
Reference Allele: GAAAlternative Allele: G,GA,GAAA
Primary Allele: GSecondary Allele: GAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTAGTGCTAACTGTGAAGTGCATGTTACACGTATCAACGACCAAGTGTAGTACATGCTTTTTTTTCTTTTGCCGCGCAAACTCTCCAGTATTAACATAA[GAA/G,GA,GAAA]
AAAAAAAATCAGAACACACACAATTTTTTTTGGTTTCTCCAAATATATAATTAATTAATTATTGTTTTCTTCAGTTAATCATATTTTTCTAGTTGGATCT

Reverse complement sequence

AGATCCAACTAGAAAAATATGATTAACTGAAGAAAACAATAATTAATTAATTATATATTTGGAGAAACCAAAAAAAATTGTGTGTGTTCTGATTTTTTTT[TTC/C,TC,TTTC]
TTATGTTAATACTGGAGAGTTTGCGCGGCAAAAGAAAAAAAAGCATGTACTACACTTGGTCGTTGATACGTGTAACATGCACTTCACAGTTAGCACTACG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.90% 38.70% 0.40% 0.00% GA: 6.24%; GAAA: 0.68%
All Indica  2759 87.90% 10.10% 0.11% 0.00% GA: 1.81%; GAAA: 0.07%
All Japonica  1512 1.90% 92.90% 1.06% 0.00% GA: 2.51%; GAAA: 1.72%
Aus  269 24.50% 0.70% 0.00% 0.00% GA: 74.72%
Indica I  595 91.80% 8.10% 0.17% 0.00% NA
Indica II  465 98.30% 1.50% 0.00% 0.00% GA: 0.22%
Indica III  913 83.60% 14.20% 0.11% 0.00% GA: 2.08%
Indica Intermediate  786 84.00% 11.80% 0.13% 0.00% GA: 3.82%; GAAA: 0.25%
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 2.40% 84.10% 2.38% 0.00% GA: 6.94%; GAAA: 4.17%
Japonica Intermediate  241 2.10% 92.90% 1.66% 0.00% GAAA: 2.07%; GA: 1.24%
VI/Aromatic  96 2.10% 94.80% 0.00% 0.00% GA: 3.12%
Intermediate  90 30.00% 62.20% 0.00% 0.00% GAAA: 4.44%; GA: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0137335979 GAA -> G LOC_Os01g64310.1 3_prime_UTR_variant ; 138.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> G LOC_Os01g64310.2 3_prime_UTR_variant ; 695.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> G LOC_Os01g64320.1 downstream_gene_variant ; 2132.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> GAAA LOC_Os01g64310.1 3_prime_UTR_variant ; 140.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> GAAA LOC_Os01g64310.2 3_prime_UTR_variant ; 697.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> GAAA LOC_Os01g64320.1 downstream_gene_variant ; 2130.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> GA LOC_Os01g64310.1 3_prime_UTR_variant ; 139.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> GA LOC_Os01g64310.2 3_prime_UTR_variant ; 696.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 N N N N
vg0137335979 GAA -> GA LOC_Os01g64320.1 downstream_gene_variant ; 2131.0bp to feature; MODIFIER silent_mutation Average:82.6; most accessible tissue: Minghui63 young leaf, score: 96.338 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)
vg0137335979 GAA G -0.05 0.1 -0.03 -0.07 0.06 0.21
vg0137335979 GAA GA 0.0 0.01 0.0 -0.03 -0.05 -0.05
vg0137335979 GAA GAAA 0.02 -0.01 0.03 0.0 -0.01 -0.01