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view test-data/sequences.tree.amino_acid.reconstruction.csv @ 3:4d8ae6baddbe draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel commit 68ea06281ba78b828b8d1947745161697dc0fbc5
author iuc
date Tue, 10 Jun 2025 13:32:13 +0000
parents d5699a62c761
children
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site,gene,direction,snp,dimer,apobec,aa_position,parent,parent_codon,parent_aa,child,child_codon,child_aa,mutation_category,score,prediction,homoplasy,occurrence
1355,OPG001_CDS_180,reverse,G->T,,False,2,Node1,ACT,T,DQ011155,AAT,N,nonsynonymous,65,moderately conservative,False,1
6600,NA,NA,G->T,,False,NA,Node1,NA,NA,DQ011155,NA,NA,intergenic,NA,NA,False,1
8973,NA,NA,C->A,,False,NA,Node1,NA,NA,DQ011155,NA,NA,intergenic,NA,NA,False,1
11363,OPG023_CDS_173,reverse,T->C,,False,2,Node1,TAT,Y,DQ011155,TGT,C,nonsynonymous,194,radical,False,1
21633,OPG034_CDS_165,reverse,C->T,AC,False,3,Node1,TTG,L,DQ011155,TTA,L,synonymous,NA,NA,False,1
35994,OPG052_CDS_148,reverse,C->G,,False,2,Node1,AGT,S,DQ011155,ACT,T,nonsynonymous,58,moderately conservative,False,1
37989,OPG054_CDS_146,reverse,T->C,,False,2,Node1,CAA,Q,DQ011155,CGA,R,nonsynonymous,43,conservative,False,1
44147,OPG062_CDS_138,forward,A->C,,False,1,Node1,AGA,R,DQ011155,CGA,R,synonymous,NA,NA,False,1
58283,OPG074_CDS_127,reverse,A->G,,False,3,Node1,GTT,V,DQ011155,GTC,V,synonymous,NA,NA,False,1
73148,OPG089_CDS_112,forward,G->A,GA,True,1,Node1,GAG,E,DQ011155,AAG,K,nonsynonymous,56,moderately conservative,False,1
83797,OPG105_CDS_96,forward,C->T,GC,False,3,Node1,AGC,S,DQ011155,AGT,S,synonymous,NA,NA,False,1
97065,OPG115_CDS_86,forward,C->T,GC,False,1,Node1,CAT,H,DQ011155,TAT,Y,nonsynonymous,83,moderately conservative,False,1
110532,OPG127_CDS_74,reverse,G->A,GT,False,1,Node1,CAT,H,DQ011155,TAT,Y,nonsynonymous,83,moderately conservative,False,1
132943,OPG151_CDS_50,forward,C->T,GC,False,3,Node1,CGC,R,DQ011155,CGT,R,synonymous,NA,NA,False,1
137411,NA,NA,G->A,GC,False,NA,Node1,NA,NA,DQ011155,NA,NA,intergenic,NA,NA,False,1
140036,OPG155_CDS_47,reverse,C->A,,False,2,Node1,AGA,R,DQ011155,ATA,I,nonsynonymous,97,moderately conservative,False,1
143163,OPG161_CDS_41,forward,C->T,CC,False,3,Node1,GCC,A,DQ011155,GCT,A,synonymous,NA,NA,False,1
159492,OPG185_CDS_24,forward,T->C,,False,3,Node1,ATT,I,DQ011155,ATC,I,synonymous,NA,NA,False,1
165893,OPG191_CDS_19,forward,G->A,GT,False,3,Node1,ATG,M,DQ011155,ATA,I,nonsynonymous,10,conservative,False,1
171132,OPG199_CDS_14,forward,G->A,GC,False,3,Node1,ATG,M,DQ011155,ATA,I,nonsynonymous,10,conservative,False,1
178028,NA,NA,C->T,GC,False,NA,Node1,NA,NA,DQ011155,NA,NA,intergenic,NA,NA,False,1
183889,OPG210_CDS_7,forward,A->C,,False,3,Node1,ACA,T,DQ011155,ACC,T,synonymous,NA,NA,False,1
241,NA,NA,A->C,,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
826,NA,NA,C->T,TC,True,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
1788,OPG002_CDS_179,reverse,G->A,GC,False,3,Node1,TGC,C,JX878413,TGT,C,synonymous,NA,NA,False,1
6100,OPG015_CDS_177,reverse,A->G,,False,2,Node1,GTA,V,JX878413,GCA,A,nonsynonymous,64,moderately conservative,False,1
8477,NA,NA,T->C,,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
11156,OPG023_CDS_173,reverse,G->A,GC,False,2,Node1,GCC,A,JX878413,GTC,V,nonsynonymous,64,moderately conservative,False,1
16178,OPG027_CDS_170,reverse,C->A,,False,3,Node1,GAG,E,JX878413,GAT,D,nonsynonymous,45,conservative,False,1
20627,NA,NA,A->G,,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
27593,NA,NA,C->T,TC,True,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
49030,OPG066_CDS_134,reverse,C->T,CC,False,3,Node1,AAG,K,JX878413,AAA,K,synonymous,NA,NA,False,1
51979,OPG068_CDS_133,forward,T->C,,False,3,Node1,TTT,F,JX878413,TTC,F,synonymous,NA,NA,False,1
54162,OPG071_CDS_130,reverse,C->T,AC,False,3,Node1,CTG,L,JX878413,CTA,L,synonymous,NA,NA,False,1
87349,OPG106_CDS_95,reverse,C->T,AC,False,3,Node1,GTG,V,JX878413,GTA,V,synonymous,NA,NA,False,1
89411,OPG109_CDS_92,reverse,T->C,,False,3,Node1,AAA,K,JX878413,AAG,K,synonymous,NA,NA,False,1
118195,OPG134_CDS_67,forward,C->T,AC,False,1,Node1,CTA,L,JX878413,TTA,L,synonymous,NA,NA,False,1
129252,OPG148_CDS_53,forward,T->C,,False,3,Node1,TGT,C,JX878413,TGC,C,synonymous,NA,NA,False,1
138312,OPG153_CDS_49,reverse,G->A,GG,False,2,Node1,CCC,P,JX878413,CTC,L,nonsynonymous,98,moderately conservative,False,1
142201,OPG160_CDS_42,reverse,G->T,,False,3,Node1,TCC,S,JX878413,TCA,S,synonymous,NA,NA,False,1
153104,NA,NA,G->A,GT,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
154113,NA,NA,G->A,GT,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
157592,NA,NA,C->A,,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
168929,NA,NA,G->T,,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
173151,OPG201_CDS_12,forward,C->T,AC,False,2,Node1,ACA,T,JX878413,ATA,I,nonsynonymous,89,moderately conservative,False,1
176367,OPG205_CDS_10,forward,C->T,AC,False,3,Node1,AAC,N,JX878413,AAT,N,synonymous,NA,NA,False,1
177394,OPG205_CDS_10,forward,C->T,TC,True,1,Node1,CGT,R,JX878413,TGT,C,nonsynonymous,180,radical,False,1
186579,OPG210_CDS_7,forward,G->T,,False,2,Node1,AGA,R,JX878413,ATA,I,nonsynonymous,97,moderately conservative,False,1
187075,NA,NA,C->G,,False,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
187738,NA,NA,C->T,TC,True,NA,Node1,NA,NA,JX878413,NA,NA,intergenic,NA,NA,False,1
190234,OPG016_CDS_5,forward,G->A,GC,False,3,Node1,TTG,L,JX878413,TTA,L,synonymous,NA,NA,False,1
190759,OPG015_CDS_4,forward,T->C,,False,2,Node1,GTA,V,JX878413,GCA,A,nonsynonymous,64,moderately conservative,False,1