Summary of assembly and annotation
 
 Scientific name   JCM no.
 Phoma herbarum   15942
Genome assembly:
ALLPATHS-LG (ver. 52488)
Genome assembly ver. 001
Estimated genome size   44,465,876
Sequence coverage   179
# of contigs   499
Total length (contigs)   38,509,753
N50 (contigs)   559,926
# of scaffolds   218
Total scaffold length (with gaps)   39,263,577
% gaps   1.9
N50 (scaffold)   1,302,950
GC%   51.7
Gene prediction:
  MAKER annotation pipeline (release 2.31.8)
    Gene predictors used: Augustus (3.0.3), SNAP (2013-02-16), GeneMark-ES (Suite 4.21)
    Reference used: Phoma tracheiphila
    tRNAscan-SE (version 1.23)
  Infernal cmscan (version 1.1.1)
    Database used: Rfam (Release 12.0)
Functional annotaion:
  Sma3S: 2013-09-01
    Database used: Uniprot-TrEMBL (release 2015_11), Uniprot-sprot (release 2015_11)
Gene prediction & funcational annotation ver. 001
# of predicted gene models   13,349
# of predicted transcript models   13,349
Average transcript length (bp)   1,504
Average coding length (bp)   1,372
Average protein length (aa)   457
Average number of exons per gene model   2.5
Average exon size (bp)   557
Average intron size (bp)   87
# of non-coding RNA   801
# of functionally annotated genes trembl   10,939
# of functionally annotated genes sprot   3,003
CEGMA complete (%)   97.18
CEGMA partial (%)   97.58

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