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Detailed information for vg0137335062:

Variant ID: vg0137335062 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 37335062
Reference Allele: AAlternative Allele: AGCGCCG
Primary Allele: ASecondary Allele: AGCGCCG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTCTACCGCGGCCGCGCGCCGTCGGGAACCAAGACCGCGTGGAAGATGAACGAGTACAGAGCATTCCACTACCCCGACGCCTCCTCCGCCTCCGCCTCC[A/AGCGCCG]
GCGCCGGCGCCGCCGCGCCACCAAACCATCTTCCTCCGCAGGTGATTAATCAATACCTAAGTACACGTTGCTTTCTTTGCCGTTGCACATACTAGCCGCA

Reverse complement sequence

TGCGGCTAGTATGTGCAACGGCAAAGAAAGCAACGTGTACTTAGGTATTGATTAATCACCTGCGGAGGAAGATGGTTTGGTGGCGCGGCGGCGCCGGCGC[T/CGGCGCT]
GGAGGCGGAGGCGGAGGAGGCGTCGGGGTAGTGGAATGCTCTGTACTCGTTCATCTTCCACGCGGTCTTGGTTCCCGACGGCGCGCGGCCGCGGTAGAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of AGCGCCG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.80% 10.20% 0.00% 0.00% NA
All Indica  2759 90.00% 10.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 26.40% 73.60% 0.00% 0.00% NA
Indica I  595 91.80% 8.20% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 85.10% 14.90% 0.00% 0.00% NA
Indica Intermediate  786 88.90% 11.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0137335062 A -> AGCGCCG LOC_Os01g64310.1 disruptive_inframe_insertion ; p.Gly157_Ala158dup; MODERATE inframe_variant Average:89.221; most accessible tissue: Minghui63 young leaf, score: 96.22 N N N N
vg0137335062 A -> AGCGCCG LOC_Os01g64310.2 disruptive_inframe_insertion ; p.Gly157_Ala158dup; MODERATE inframe_variant Average:89.221; most accessible tissue: Minghui63 young leaf, score: 96.22 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)
vg0137335062 A AGCGC* 0.03 -0.11 -0.19 -0.14 -0.28 -0.25