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Detailed information for vg1100960277:

Variant ID: vg1100960277 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 960277
Reference Allele: GTTAlternative Allele: GT,G,GTTT
Primary Allele: GTSecondary Allele: GTT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACTGAGAAGATGGCATTTCAACAACAAAAAAGAAAAAAATAGTCAAGGTAAAAACGAATTAAGGTTACCATAAATTCTTATACATAAGATAAAAAGCAT[GTT/GT,G,GTTT]
TTTTTTTTCTTCATATTGAATTTTCAGCATTCACGGAGATGGTTGGATGAAAGAGAGCTAATCATGTTGAAATACGTTTAGGAAAGCTATAATCACAAAC

Reverse complement sequence

GTTTGTGATTATAGCTTTCCTAAACGTATTTCAACATGATTAGCTCTCTTTCATCCAACCATCTCCGTGAATGCTGAAAATTCAATATGAAGAAAAAAAA[AAC/AC,C,AAAC]
ATGCTTTTTATCTTATGTATAAGAATTTATGGTAACCTTAATTCGTTTTTACCTTGACTATTTTTTTCTTTTTTGTTGTTGAAATGCCATCTTCTCAGTT

Allele Frequencies:

Populations Population SizeFrequency of GT(primary allele) Frequency of GTT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.50% 34.80% 0.55% 0.00% G: 0.08%; GTTT: 0.04%
All Indica  2759 95.40% 3.70% 0.83% 0.00% G: 0.04%
All Japonica  1512 2.80% 97.10% 0.00% 0.00% GTTT: 0.13%
Aus  269 97.00% 2.60% 0.37% 0.00% NA
Indica I  595 98.00% 0.70% 1.34% 0.00% NA
Indica II  465 86.50% 12.70% 0.86% 0.00% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 94.00% 4.60% 1.27% 0.00% G: 0.13%
Temperate Japonica  767 2.90% 96.90% 0.00% 0.00% GTTT: 0.26%
Tropical Japonica  504 1.60% 98.40% 0.00% 0.00% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 42.20% 52.20% 2.22% 0.00% G: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1100960277 GTT -> GTTT LOC_Os11g02850.1 upstream_gene_variant ; 1384.0bp to feature; MODIFIER silent_mutation Average:72.546; most accessible tissue: Zhenshan97 flower, score: 88.727 N N N N
vg1100960277 GTT -> GTTT LOC_Os11g02840.1 intron_variant ; MODIFIER silent_mutation Average:72.546; most accessible tissue: Zhenshan97 flower, score: 88.727 N N N N
vg1100960277 GTT -> GT LOC_Os11g02850.1 upstream_gene_variant ; 1385.0bp to feature; MODIFIER silent_mutation Average:72.546; most accessible tissue: Zhenshan97 flower, score: 88.727 N N N N
vg1100960277 GTT -> GT LOC_Os11g02840.1 intron_variant ; MODIFIER silent_mutation Average:72.546; most accessible tissue: Zhenshan97 flower, score: 88.727 N N N N
vg1100960277 GTT -> G LOC_Os11g02850.1 upstream_gene_variant ; 1386.0bp to feature; MODIFIER silent_mutation Average:72.546; most accessible tissue: Zhenshan97 flower, score: 88.727 N N N N
vg1100960277 GTT -> G LOC_Os11g02840.1 intron_variant ; MODIFIER silent_mutation Average:72.546; most accessible tissue: Zhenshan97 flower, score: 88.727 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)
vg1100960277 GTT G 0.06 -0.08 0.01 -0.13 -0.08 -0.04
vg1100960277 GTT GT -0.01 0.01 0.01 -0.06 -0.04 -0.1
vg1100960277 GTT GTTT -0.04 -0.05 -0.01 0.01 -0.03 -0.14