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Detailed information for vg0135122946:

Variant ID: vg0135122946 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 35122946
Reference Allele: ACAGAlternative Allele: A
Primary Allele: ASecondary Allele: ACAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAGTGAGCTAGCCAAGTACCTTCTGTGATCTCTTTCCCACACGATCGAGCTGGATTAGTATTTCGGGAGATGAGATGAGGAGGAGGAGGAGAATCAACA[ACAG/A]
CAAGTGGAGTTGAGCCGTAGTAGTAGTAGCAGTAGACAGCGATCCGTCGCGAGATGCCACGAGAGATTTATAATGGGTGCAACACCAACACCGGCACACC

Reverse complement sequence

GGTGTGCCGGTGTTGGTGTTGCACCCATTATAAATCTCTCGTGGCATCTCGCGACGGATCGCTGTCTACTGCTACTACTACTACGGCTCAACTCCACTTG[CTGT/T]
TGTTGATTCTCCTCCTCCTCCTCATCTCATCTCCCGAAATACTAATCCAGCTCGATCGTGTGGGAAAGAGATCACAGAAGGTACTTGGCTAGCTCACTCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of ACAG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.00% 35.90% 0.02% 0.00% NA
All Indica  2759 97.20% 2.80% 0.00% 0.00% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.30% 0.00% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.40% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 42.20% 56.70% 1.11% 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
vg0135122946 ACAG -> A LOC_Os01g60730.1 5_prime_UTR_variant ; 332.0bp to feature; MODIFIER silent_mutation Average:99.639; most accessible tissue: Callus, score: 99.9 N N N N
vg0135122946 ACAG -> A LOC_Os01g60730.2 5_prime_UTR_variant ; 332.0bp to feature; MODIFIER silent_mutation Average:99.639; most accessible tissue: Callus, score: 99.9 N N N N
vg0135122946 ACAG -> A LOC_Os01g60720.1 upstream_gene_variant ; 2947.0bp to feature; MODIFIER silent_mutation Average:99.639; most accessible tissue: Callus, score: 99.9 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)
vg0135122946 ACAG A -0.07 0.05 0.16 0.02 0.09 0.15