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Detailed information for vg0620020001:

Variant ID: vg0620020001 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 20020001
Reference Allele: TAlternative Allele: TTCACTAG
Primary Allele: TSecondary Allele: TTCACTAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCGGAGAAGGTCACCGCGAAATCCTCCGCCGCCGCCGCGACGGTCTCCTCCACCGACGTGCTGCCGCCGGTGTGAAACGCTAATTCACCTTGCTTGGTG[T/TTCACTAG]
TCACTACTAACATCACCTAGTGTTGTTATTACTGCGTCACTGTACATTAATTCCGAATGTTCTACCACTTGGTATACTAACTAATTAGCATTTCCAAACC

Reverse complement sequence

GGTTTGGAAATGCTAATTAGTTAGTATACCAAGTGGTAGAACATTCGGAATTAATGTACAGTGACGCAGTAATAACAACACTAGGTGATGTTAGTAGTGA[A/CTAGTGAA]
CACCAAGCAAGGTGAATTAGCGTTTCACACCGGCGGCAGCACGTCGGTGGAGGAGACCGTCGCGGCGGCGGCGGAGGATTTCGCGGTGACCTTCTCCGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TTCACTAG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.50% 7.50% 0.02% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 77.40% 22.50% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 88.00% 11.90% 0.13% 0.00% NA
Tropical Japonica  504 75.60% 24.40% 0.00% 0.00% NA
Japonica Intermediate  241 47.70% 52.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0620020001 T -> TTCACTAG LOC_Os06g34410.1 downstream_gene_variant ; 4999.0bp to feature; MODIFIER silent_mutation Average:89.396; most accessible tissue: Zhenshan97 flower, score: 98.194 N N N N
vg0620020001 T -> TTCACTAG LOC_Os06g34400.1 intron_variant ; MODIFIER silent_mutation Average:89.396; most accessible tissue: Zhenshan97 flower, score: 98.194 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)
vg0620020001 T TTCAC* 0.08 0.18 0.2 0.02 0.06 -0.14