Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0429661279:

Variant ID: vg0429661279 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 29661279
Reference Allele: TGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGGAlternative Allele: TGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG,T,TGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG,TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG,TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG
Primary Allele: TGCGGCGGCGGCGGCGGCGG CGGCGCCGCTGCCGCCTGTG TCCAGCCAGCGGCTGCGGTG GTGGSecondary Allele: TGCGGCGGCGGCGCCGCTGC CGCCTGTGTCCAGCCAGCGG CTGCGGTGGTGG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTATACTGATGAGACGGATGATTCGTATGTGCAGGTGTCCGAGGCCAAGAAGACGTGGTAGCAGAGTCTGACAAGAGCACGTCTCGAGCAGATGGAAC[TGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG/TGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG,T,TGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG,TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG,TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG]
GCGGTGGTCCTTGCCAACATCGTGTTCGTCCTCGGCGGGCAGAGCGTGGCCACGCTCCTCGGCCGGATTTACTACGACCAGGGCGGCGGCAGCTTGTGGC

Reverse complement sequence

GCCACAAGCTGCCGCCGCCCTGGTCGTAGTAAATCCGGCCGAGGAGCGTGGCCACGCTCTGCCCGCCGAGGACGAACACGATGTTGGCAAGGACCACCGC[CCACCACCGCAGCCGCTGGCTGGACACAGGCGGCAGCGGCGCCGCCGCCGCCGCCGCCGCCGCA/CCACCACCGCAGCCGCTGGCTGGACACAGGCGGCAGCGGCGCCGCCGCCGCA,A,CCACCACCGCAGCCGCTGGCTGGACACAGGCGGCAGCGGCGCCGCCGCCGCCGCCGCCGCCGCCGCA,CCACCACCGCAGCCGCTGGCTGGACACAGGCGGCAGCGGCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCA,CCACCACCGCAGCCGCTGGCTGGACACAGGCGGCAGCGGCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCA]
GTTCCATCTGCTCGAGACGTGCTCTTGTCAGACTCTGCTACCACGTCTTCTTGGCCTCGGACACCTGCACATACGAATCATCCGTCTCATCAGTATAAAA

Allele Frequencies:

Populations Population SizeFrequency of TGCGGCGGCGGCGGCGGCGG CGGCGCCGCTGCCGCCTGTG TCCAGCCAGCGGCTGCGGTG GTGG(primary allele) Frequency of TGCGGCGGCGGCGCCGCTGC CGCCTGTGTCCAGCCAGCGG CTGCGGTGGTGG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 0.90% 0.04% 0.00% TGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG: 0.06%; TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG: 0.02%; TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG: 0.02%; T: 0.02%
All Indica  2759 99.80% 0.20% 0.00% 0.00% T: 0.04%
All Japonica  1512 97.40% 2.40% 0.13% 0.00% NA
Aus  269 98.90% 0.00% 0.00% 0.00% TGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG: 0.37%; TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG: 0.37%; TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG: 0.37%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.80% 0.10% 0.00% 0.00% T: 0.11%
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 7.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 0.00% 0.00% TGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0429661279 TGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG -> TGCGGCGGCGGCGGCGGCGGCGGCGGCGGC GGCGGCGCCGCTGCCGCCTGTGTCCAGCCA GCGGCTGCGGTGGTGG LOC_Os04g49748.1 inframe_insertion ; p.Ala56_Ala59dup; MODERATE inframe_variant Average:92.748; most accessible tissue: Zhenshan97 flag leaf, score: 97.876 N N N N
vg0429661279 TGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG -> TGCGGCGGCGGCGCCGCTGCCGCCTGTGTC CAGCCAGCGGCTGCGGTGGTGG LOC_Os04g49748.1 inframe_deletion ; p.Ala56_Ala59del; MODERATE inframe_variant Average:92.748; most accessible tissue: Zhenshan97 flag leaf, score: 97.876 N N N N
vg0429661279 TGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG -> TGCGGCGGCGGCGGCGGCGGCGGCGGCGCC GCTGCCGCCTGTGTCCAGCCAGCGGCTGCG GTGGTGG LOC_Os04g49748.1 inframe_insertion ; p.Ala59dup; MODERATE inframe_variant Average:92.748; most accessible tissue: Zhenshan97 flag leaf, score: 97.876 N N N N
vg0429661279 TGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG -> TGCGGCGGCGGCGGCGGCGGCGGCGGCGGC GGCGGCGGCGCCGCTGCCGCCTGTGTCCAG CCAGCGGCTGCGGTGGTGG LOC_Os04g49748.1 inframe_insertion ; p.Ala55_Ala59dup; MODERATE inframe_variant Average:92.748; most accessible tissue: Zhenshan97 flag leaf, score: 97.876 N N N N
vg0429661279 TGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG -> T LOC_Os04g49748.1 disruptive_inframe_deletion ; p.Ala53_Ala73del; MODERATE inframe_variant Average:92.748; most accessible tissue: Zhenshan97 flag leaf, score: 97.876 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)
vg0429661279 TGCGG* T 0.04 -0.17 -0.21 0.0 -0.02 -0.32
vg0429661279 TGCGG* TGCGG* 0.15 0.34 0.08 -0.03 0.18 0.1