Version Differences for Read Depths

(→Evaluation)
(→Evaluation)
Line 77:
  We have evaluated the assemblies with [http://bioinf.spbau.ru/en/quast QUAST 2.2](reference genome and genes下載).    We have evaluated the assemblies with [http://bioinf.spbau.ru/en/quast QUAST 2.2](reference genome and genes下載). 
       
- Single SMRT cell reads corrected with raw, 100X and 118X short reads.   + Single SMRT cell reads were corrected with raw, 100X and 118X short reads.  
  {| {{table}} border="１"    {| {{table}} border="１" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference''' 
Line 120:
  |}    |} 
       
- Two SMRT cell reads corrected with raw, 100X, and 118X short reads. The PBcR were then filtered to 25X or directly assembled by runCA.   + Two SMRT cell reads were corrected with raw, 100X, and 118X short reads. The PBcR were then filtered to 25X or directly assembled by runCA.  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference''' 
Line 161:
  |-    |- 
  | NGA50||418393||405538||235822||193833||194196||199657    | NGA50||418393||405538||235822||193833||194196||199657 
    + |-  
    + |}  
       
    + Three SMRT cells reads were corrected with raw, 100X, and 118 short reads. The PBcR were then filtered to 25X or directly assembled by runCA.  
    + {| {{table}} border=1"1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''3_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||219||74||98||32||86||39  
    + |-  
    + | Largest contig||771076||1426293||981874||822480||1091515||520962  
    + |-  
    + | Total length||5873961||5171438||5051244||4730819||4906749||4668968  
    + |-  
    + | N50||247798||317846||413464||600008||286035||218547  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||25||10||22||8||25||11  
    + |-  
    + | Misassembled contigs length||1361077||1372143||2201123||1855654||1800186||1350243  
    + |-  
    + | Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||4.03||2.5||2.030||1.5||4.71||5.45  
    + |-  
    + | # indels per 100 kbp||1.68||0.97||5.64||3.3||4.13||3.86  
    + |-  
    + | # N's per 100 kbp||0.34||0.140||0.46||0.11||0.18||0.02  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||100||100||99.733||99.197||99.69||98.93  
    + |-  
    + | Duplication ratio||1.268||1.116||1.092||1.028||1.063||1.018  
    + |-  
    + | # genes||4494 + 3 part||4495 + 2 part||4484 + 9 part||4460 + 19 part||4468 + 20 part||4427 + 35 part  
    + |-  
    + | NGA50||286997||323732||348693||599239||286035||193471  
  |-    |- 
  |}    |}