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Detailed information for vg0625198292:

Variant ID: vg0625198292 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 25198292
Reference Allele: GAlternative Allele: GCTGT
Primary Allele: GSecondary Allele: Unkown

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGAGCTCATCGCGTCGCGCTCTTCTCGACGAGCTCCAATTTCAGGCAAGATGTCGATGCTGCCGCGCTTCCTCCTCCTCGTCGTGCTGCTCGCGGTGCC[G/GCTGT]
ATGACGGCGGCGCAGCAGCAGTACGAGGCCAACGCGCAGGGCGACTGCTACACCGACAACGGCAGCTCCGTCCTCGGCTACACCTGCGGCACCGCCGCCT

Reverse complement sequence

AGGCGGCGGTGCCGCAGGTGTAGCCGAGGACGGAGCTGCCGTTGTCGGTGTAGCAGTCGCCCTGCGCGTTGGCCTCGTACTGCTGCTGCGCCGCCGTCAT[C/ACAGC]
GGCACCGCGAGCAGCACGACGAGGAGGAGGAAGCGCGGCAGCATCGACATCTTGCCTGAAATTGGAGCTCGTCGAGAAGAGCGCGACGCGATGAGCTCGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of Unkown(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.60% 0.00% 0.91% 8.48% NA
All Indica  2759 98.30% 0.00% 0.18% 1.49% NA
All Japonica  1512 74.40% 0.00% 2.31% 23.28% NA
Aus  269 98.90% 0.00% 1.12% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.20% 0.00% 0.43% 2.37% NA
Indica III  913 99.70% 0.00% 0.00% 0.33% NA
Indica Intermediate  786 96.20% 0.00% 0.38% 3.44% NA
Temperate Japonica  767 88.80% 0.00% 0.26% 10.95% NA
Tropical Japonica  504 63.50% 0.00% 4.37% 32.14% NA
Japonica Intermediate  241 51.50% 0.00% 4.56% 43.98% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 0.00% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0625198292 G -> GCTGT LOC_Os06g41980.1 frameshift_variant ; p.Met18fs; HIGH N Average:95.273; most accessible tissue: Zhenshan97 young leaf, score: 97.085 N N N N
vg0625198292 G -> GCTGT LOC_Os06g41990.1 downstream_gene_variant ; 1983.0bp to feature; MODIFIER N Average:95.273; most accessible tissue: Zhenshan97 young leaf, score: 97.085 N N N N
vg0625198292 G -> GCTGT LOC_Os06g41990.2 downstream_gene_variant ; 1983.0bp to feature; MODIFIER N Average:95.273; most accessible tissue: Zhenshan97 young leaf, score: 97.085 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)
vg0625198292 G GCTGT 0.1 -0.17 -0.12 0.05 0.04 0.06