Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0432301781:

Variant ID: vg0432301781 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 32301781
Reference Allele: GAlternative Allele: GGTA
Primary Allele: GSecondary Allele: GGTA

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAATTACAGATCTGACTATCATTCAGTAACAAGTGGTAAGTATTAAGTACAAACTAGATTGCTACCATTTCTTCCATCATTTCGATCATAAATTTTAC[G/GGTA]
GTGCAGTATCAAAAGAACAGAACACCTTTCTCCCAGAAAGTTTGGATCTTAAATTGATGACACGGCCGGATTTTTGCGTGCATGACCGTAAAAGTGGTCA

Reverse complement sequence

TGACCACTTTTACGGTCATGCACGCAAAAATCCGGCCGTGTCATCAATTTAAGATCCAAACTTTCTGGGAGAAAGGTGTTCTGTTCTTTTGATACTGCAC[C/TACC]
GTAAAATTTATGATCGAAATGATGGAAGAAATGGTAGCAATCTAGTTTGTACTTAATACTTACCACTTGTTACTGAATGATAGTCAGATCTGTAATTCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GGTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.00% 25.60% 0.17% 0.30% NA
All Indica  2759 57.40% 41.90% 0.25% 0.51% NA
All Japonica  1512 97.80% 2.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 26.10% 72.90% 0.50% 0.50% NA
Indica II  465 67.70% 32.00% 0.00% 0.22% NA
Indica III  913 70.00% 29.00% 0.11% 0.88% NA
Indica Intermediate  786 60.30% 39.10% 0.38% 0.25% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 94.60% 5.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0432301781 G -> DEL N N silent_mutation Average:62.568; most accessible tissue: Minghui63 panicle, score: 89.702 N N N N
vg0432301781 G -> GGTA LOC_Os04g54240.1 3_prime_UTR_variant ; 312.0bp to feature; MODIFIER silent_mutation Average:62.568; most accessible tissue: Minghui63 panicle, score: 89.702 N N N N
vg0432301781 G -> GGTA LOC_Os04g54230.1 upstream_gene_variant ; 3650.0bp to feature; MODIFIER silent_mutation Average:62.568; most accessible tissue: Minghui63 panicle, score: 89.702 N N N N
vg0432301781 G -> GGTA LOC_Os04g54250.1 downstream_gene_variant ; 3035.0bp to feature; MODIFIER silent_mutation Average:62.568; most accessible tissue: Minghui63 panicle, score: 89.702 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)
vg0432301781 G GGTA -0.09 0.0 -0.11 -0.02 -0.04 -0.03