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Detailed information for vg1200761425:

Variant ID: vg1200761425 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 761425
Reference Allele: CTATAAlternative Allele: CTA,C
Primary Allele: CTATASecondary Allele: CTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGCAAATGCGGCGTCAACGTTGGCTTCCCCATCAGCCTCTCCACCGACTGCAACAAGTATATCATCTCTCTTTATTATGACGTCCCCCCCCTCTCTCT[CTATA/CTA,C]
TATATACACACATATATCTCTTTATTTTTTAGTGCTATCTAAATACTCCTCCGTTTCAGGTTATATGACGTTTTAACTTTGGTTAAAGTCAAACTACTCT

Reverse complement sequence

AGAGTAGTTTGACTTTAACCAAAGTTAAAACGTCATATAACCTGAAACGGAGGAGTATTTAGATAGCACTAAAAAATAAAGAGATATATGTGTGTATATA[TATAG/TAG,G]
AGAGAGAGGGGGGGGACGTCATAATAAAGAGAGATGATATACTTGTTGCAGTCGGTGGAGAGGCTGATGGGGAAGCCAACGTTGACGCCGCATTTGCCGG

Allele Frequencies:

Populations Population SizeFrequency of CTATA(primary allele) Frequency of CTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.50% 3.70% 15.59% 7.19% C: 0.02%
All Indica  2759 61.20% 5.10% 22.83% 10.80% NA
All Japonica  1512 97.40% 0.00% 1.06% 1.46% C: 0.07%
Aus  269 53.20% 11.90% 29.37% 5.58% NA
Indica I  595 92.30% 0.70% 4.87% 2.18% NA
Indica II  465 40.00% 2.20% 38.49% 19.35% NA
Indica III  913 56.70% 9.40% 23.77% 10.08% NA
Indica Intermediate  786 55.50% 5.30% 26.08% 13.10% NA
Temperate Japonica  767 96.50% 0.00% 1.43% 2.09% NA
Tropical Japonica  504 98.20% 0.00% 0.79% 0.79% C: 0.20%
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% NA
VI/Aromatic  96 97.90% 1.00% 0.00% 1.04% NA
Intermediate  90 81.10% 1.10% 13.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1200761425 CTATA -> C LOC_Os12g02350.1 upstream_gene_variant ; 2365.0bp to feature; MODIFIER silent_mutation Average:62.355; most accessible tissue: Zhenshan97 flower, score: 93.87 N N N N
vg1200761425 CTATA -> C LOC_Os12g02340.1 intron_variant ; MODIFIER silent_mutation Average:62.355; most accessible tissue: Zhenshan97 flower, score: 93.87 N N N N
vg1200761425 CTATA -> C LOC_Os12g02340.2 intron_variant ; MODIFIER silent_mutation Average:62.355; most accessible tissue: Zhenshan97 flower, score: 93.87 N N N N
vg1200761425 CTATA -> DEL N N silent_mutation Average:62.355; most accessible tissue: Zhenshan97 flower, score: 93.87 N N N N
vg1200761425 CTATA -> CTA LOC_Os12g02350.1 upstream_gene_variant ; 2363.0bp to feature; MODIFIER silent_mutation Average:62.355; most accessible tissue: Zhenshan97 flower, score: 93.87 N N N N
vg1200761425 CTATA -> CTA LOC_Os12g02340.1 intron_variant ; MODIFIER silent_mutation Average:62.355; most accessible tissue: Zhenshan97 flower, score: 93.87 N N N N
vg1200761425 CTATA -> CTA LOC_Os12g02340.2 intron_variant ; MODIFIER silent_mutation Average:62.355; most accessible tissue: Zhenshan97 flower, score: 93.87 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)
vg1200761425 CTATA C -0.15 -0.04 -0.07 -0.08 -0.11 -0.1
vg1200761425 CTATA CTA 0.09 0.04 -0.03 0.08 0.06 -0.27