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Detailed information for vg0418998002:

Variant ID: vg0418998002 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 18998002
Reference Allele: GAlternative Allele: GGCA
Primary Allele: GSecondary Allele: GGCA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAATCAAATTGTTTCCACAGCTGCATTACCTGAAACTGAAACCTCCCAAATTTCAGTTCAAAACGAGCTGCTCGAGATGGCATCGATGGCGATGAACAAT[G/GGCA]
GCAGCAGCAGCAGCACCATCGCCCTAGTCTATGACGATGGGGGTGGCCGAGGTGTAGCCGCCGGCGCGGCCCCGGATCCTCGCCGGGATCTCCGCGCGGA

Reverse complement sequence

TCCGCGCGGAGATCCCGGCGAGGATCCGGGGCCGCGCCGGCGGCTACACCTCGGCCACCCCCATCGTCATAGACTAGGGCGATGGTGCTGCTGCTGCTGC[C/TGCC]
ATTGTTCATCGCCATCGATGCCATCTCGAGCAGCTCGTTTTGAACTGAAATTTGGGAGGTTTCAGTTTCAGGTAATGCAGCTGTGGAAACAATTTGATTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GGCA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 2.00% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 95.10% 4.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 90.60% 9.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0418998002 G -> GGCA LOC_Os04g31730.1 3_prime_UTR_variant ; 23.0bp to feature; MODIFIER silent_mutation Average:70.425; most accessible tissue: Callus, score: 85.546 N N N N
vg0418998002 G -> GGCA LOC_Os04g31740.1 upstream_gene_variant ; 3348.0bp to feature; MODIFIER silent_mutation Average:70.425; most accessible tissue: Callus, score: 85.546 N N N N
vg0418998002 G -> GGCA LOC_Os04g31710.1 downstream_gene_variant ; 2312.0bp to feature; MODIFIER silent_mutation Average:70.425; most accessible tissue: Callus, score: 85.546 N N N N
vg0418998002 G -> GGCA LOC_Os04g31720.1 downstream_gene_variant ; 1427.0bp to feature; MODIFIER silent_mutation Average:70.425; most accessible tissue: Callus, score: 85.546 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)
vg0418998002 G GGCA -0.01 -0.03 -0.04 0.04 0.03 0.07