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Detailed information for vg1100141257:

Variant ID: vg1100141257 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 141257
Reference Allele: GGGAAlternative Allele: GGGAGGA,G
Primary Allele: GGGASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGAACTAAACACACCCCTAGTTAACATCCTGTGGCGACGGAGGGGGAAAAAAATAATAGGAGATGGGCAGCAGCGCCAAGCTTCCTTTGGTGGATATTG[GGGA/GGGAGGA,G]
GGAGGAGGAGGCGTTGGTGTTTGAAGATGAGGAGAAGACCGAGCTGATTAGGGTGCAAGACTTCCGTCGCGTCTGGGAACATCGCTTTAACAGCTAAGGG

Reverse complement sequence

CCCTTAGCTGTTAAAGCGATGTTCCCAGACGCGACGGAAGTCTTGCACCCTAATCAGCTCGGTCTTCTCCTCATCTTCAAACACCAACGCCTCCTCCTCC[TCCC/TCCTCCC,C]
CAATATCCACCAAAGGAAGCTTGGCGCTGCTGCCCATCTCCTATTATTTTTTTCCCCCTCCGTCGCCACAGGATGTTAACTAGGGGTGTGTTTAGTTCAC

Allele Frequencies:

Populations Population SizeFrequency of GGGA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.90% 0.10% 0.00% 0.00% GGGAGGA: 0.02%
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.00% 0.00% GGGAGGA: 0.37%
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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 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
vg1100141257 GGGA -> GGGAGGA LOC_Os11g01260.1 disruptive_inframe_insertion ; p.Glu17dup; MODERATE N Average:65.874; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141257 GGGA -> GGGAGGA LOC_Os11g01250.1 upstream_gene_variant ; 943.0bp to feature; MODIFIER N Average:65.874; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141257 GGGA -> GGGAGGA LOC_Os11g01240.1 downstream_gene_variant ; 2302.0bp to feature; MODIFIER N Average:65.874; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141257 GGGA -> GGGAGGA LOC_Os11g01270.1 downstream_gene_variant ; 2904.0bp to feature; MODIFIER N Average:65.874; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141257 GGGA -> G LOC_Os11g01260.1 disruptive_inframe_deletion ; p.Glu17del; MODERATE N Average:65.874; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141257 GGGA -> G LOC_Os11g01250.1 upstream_gene_variant ; 940.0bp to feature; MODIFIER N Average:65.874; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141257 GGGA -> G LOC_Os11g01240.1 downstream_gene_variant ; 2299.0bp to feature; MODIFIER N Average:65.874; most accessible tissue: Callus, score: 88.234 N N N N
vg1100141257 GGGA -> G LOC_Os11g01270.1 downstream_gene_variant ; 2907.0bp to feature; MODIFIER N Average:65.874; most accessible tissue: Callus, score: 88.234 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)
vg1100141257 GGGA G 0.14 0.07 0.09 0.09 0.12 0.11
vg1100141257 GGGA GGGAG* 0.1 0.09 0.12 -0.01 0.06 0.08