Version Differences for Read Depths

(→Evaluation)
(→Evaluation)
Line 166:
  |}    |} 
       
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''2_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||106||80||81||71||81||54  
    + |-  
    + | Largest contig||762045||757702||767781||405645||520095||570062  
    + |-  
    + | Total length||5168000||5080370||4918962||4799524||4832961||4725680  
    + |-  
    + | N50||419161||405539||331262||193986||186504||210927  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||13||18||15||9||16||16  
    + |-  
    + | Misassembled contigs length||1591856||1751860||1703983||165469||616747||1468075  
    + |-  
    + | Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||2.44||1.83||5.08||4.34||6.28||6.08  
    + |-  
    + | # indels per 100 kbp||0.88||0.82||6.34||2.14||5.61||2.93  
    + |-  
    + | # N's per 100 kbp||0.48||0.04||0.94||0.02||0.43||0.08  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||100||100||99.652||98.76||99.567||99.194  
    + |-  
    + | Duplication ratio||1.116||1.098||1.065||1.048||1.047||1.028  
    + |-  
    + | # genes||4495 + 2 part||4495 + 2 part||4475 + 16 part||4432 + 31 part||4458 + 30 part||4434 + 43 part  
    + |-  
    + | 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.    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"    {| {{table}} border=1"1"