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Detailed information for vg0526683815:

Variant ID: vg0526683815 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 26683815
Reference Allele: GCTAAlternative Allele: G
Primary Allele: GCTASecondary Allele: G

Inferred Ancestral Allele : GCTA (evidence from allele frequency in Oryza rufipogon: GCTA: 0.99, G: 0.02, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CCGCTTCTTCGTCGCCGGCACGCAGCCGCCAGGTTCTCTCAATTAACCGCGCGCGTACGGTTAATTTGATCGATCGGGTCAGCCATGGGACTTTTCCAAT[GCTA/G]
GCTAGCTAATAGTGTAGGTGTTCTGGGCCGGATTCTTGATCGAGATAGCAGCCTCTTGATTGAGATGCCCAGATGGGTCATTTTGGATGTAGCTGGATCT

Reverse complement sequence

AGATCCAGCTACATCCAAAATGACCCATCTGGGCATCTCAATCAAGAGGCTGCTATCTCGATCAAGAATCCGGCCCAGAACACCTACACTATTAGCTAGC[TAGC/C]
ATTGGAAAAGTCCCATGGCTGACCCGATCGATCAAATTAACCGTACGCGCGCGGTTAATTGAGAGAACCTGGCGGCTGCGTGCCGGCGACGAAGAAGCGG

Allele Frequencies:

Populations Population SizeFrequency of GCTA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 5.20% 0.00% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 23.00% 77.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0526683815 GCTA -> G LOC_Os05g46020.1 3_prime_UTR_variant ; 56.0bp to feature; MODIFIER silent_mutation Average:96.128; most accessible tissue: Zhenshan97 flag leaf, score: 98.537 N N N N
vg0526683815 GCTA -> G LOC_Os05g46030.1 upstream_gene_variant ; 2163.0bp to feature; MODIFIER silent_mutation Average:96.128; most accessible tissue: Zhenshan97 flag leaf, score: 98.537 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)
vg0526683815 GCTA G -0.1 -0.04 0.12 0.04 -0.08 -0.15