[maker-devel] exon numbering bug?

[Kang, Yang Jae]

Hello

 

I want to check this is bug or my misunderstanding. The following is the
gff3 result of maker pipeline. 

I think those red marks should be mRNA-2. This type of error was found only
at exon

 

scaffold_22        maker   mRNA   604856  612126  .          +         .
ID=211342;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2;Parent=211320

scaffold_22        maker   exon     604856  605185  0.51      +         .
ID=211343;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2788;Parent
=211342

scaffold_22        maker   exon     608362  608456  0.51      +         .
ID=211344;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2791;Parent
=211342

scaffold_22        maker   exon     610193  610286  0.51      +         .
ID=211345;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2792;Parent
=211342

scaffold_22        maker   exon     610583  610714  0.51      +         .
ID=211346;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2793;Parent
=211342

scaffold_22        maker   exon     610838  610942  0.51      +         .
ID=211347;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2794;Parent
=211342

scaffold_22        maker   exon     611458  612126  0.51      +         .
ID=211348;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2795;Parent
=211342

scaffold_22        maker   five_prime_UTR   604856  604972  .          +
.
ID=211349;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:UTR1;Parent=2113
42

scaffold_22        maker   CDS      604973  605185  .          +         0
ID=211350;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2905;Parent=
211342

scaffold_22        maker   CDS      608362  608456  .          +         0
ID=211351;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2906;Parent=
211342

scaffold_22        maker   CDS      610193  610286  .          +         1
ID=211352;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2907;Parent=
211342

scaffold_22        maker   CDS      610583  610714  .          +         0
ID=211353;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2908;Parent=
211342

scaffold_22        maker   CDS      610838  610942  .          +         0
ID=211354;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2909;Parent=
211342

scaffold_22        maker   CDS      611458  611661  .          +         0
ID=211355;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2910;Parent=
211342

scaffold_22        maker   three_prime_UTR 611662  612126  .          +
.
ID=211356;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:UTR2;Parent=2113
42

scaffold_22        maker   start_codon       604973  604975  .          +
.
ID=211357;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:start1;Parent=21
1342

scaffold_22        maker   stop_codon       611659  611661  .          +
.
ID=211358;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:stop2;Parent=211
342

 

Thank you!

 

Kang, Yang Jae 

Ph.D.

Cropgenomics Lab.

College of Agriculture and Life Science

Seoul National University 

Korea

 

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