Files for assembly Zm-W22-REFERENCE-NRGENE-2.0

Files:
 Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1._association.txt
    Generated on 17-Dec-2017 by Maggie Woodhouse, MaizeGDB, 
    using CoGe SynMap, with the following parameters:
      #CDS/CDS
      #Megablast, 0.001 e-value
      #Maximum distance between two matches (-D): 20 genes
      #Minimum number of aligned pairs (-A): 3 genes
      #QuotaAlign 1:1

    Only associations that share the same chromosome are selected. 
    For instance, if a GRMZM gene is on Chromosome 3 and its putative 
    W22 syntelog is on Chromosome 1, the association is not included. 
    Cases where the W22 gene annotation is merged or split is noted 
    in Column 3. In such cases either the GRMZM or the W22 gene has 
    two genes in the column. For instance, if the W22 gene is split 
    relative to its GRMZM counterpart, the split genes are both 
    represented in the W22 column.

  W22.allTE.withSolo_10Jan18.gff3.gz 
    Contains transposable elements annotated on W22

  Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.cdna.fa.gz
    cDNA sequence for annotation Zm00004b for assembly 
    Zm-W22-REFERENCE-NRGENE-2.0

  Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.cds.fa.gz
    CDS sequence for annotation Zm00004b for assembly
    Zm-W22-REFERENCE-NRGENE-2.0

  Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.gene.fa.gz
    Genomic sequence for annotation Zm00004b for assembly
    Zm-W22-REFERENCE-NRGENE-2.0

  Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.gff3
    zea_maysw22_core_53_87_12.gff (Josh Stein, Gramene) -->
      Zm-W22-REFERENCE-NRGENE-2.0.gff -->
        Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.gff3
    Annotations on unplaced scaffolds with the designation 
    "10000001" were replaced with the scaffold ID from the file

  Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.protein.fa.gz
    Protein sequence for annotation Zm00004b for assembly
    Zm-W22-REFERENCE-NRGENE-2.0

  Zm-W22-REFERENCE-NRGENE-2.0.fa.gz
    Zm-W22-REFERENCE-NRGENE-2.0 pseudomolecule sequence with all
    unplaced scaffolds in "unmapped".

  Zm-W22-REFERENCE-NRGENE-2.0.chr_scaffolds.fa.gz
    Zm-W22-REFERENCE-NRGENE-2.0 pseudomolecule sequence with
    individual scaffolds

  Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.chr_scaffolds.gff3.gz
    Zm-W22-REFERENCE-NRGENE-2.0 annotation placed on individual
    scaffolds.

  Zm-W22-REFERENCE-NRGENE-2.0.scaffolds.fa.gz
    All scaffolds in the Zm-W22-REFERENCE-NRGENE-2.0 genome assembly,
    no psuedomolecules
  
 
NOTE: Unable to create index files for Zm-W22-REFERENCE-NRGENE-2.0.fa due to an error in the FASTA file.