Version Differences for Read Depths

Revision as of 13 August 2013 20:53

(→Performance)

Revision as of 13 August 2013 20:57

(→Evaluation)

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 								Two SMRT cell reads corrected with raw, 100X, and 118X short reads. The PBcR were then filtered to 25X or directly assembled by runCA.
 								{| {{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
 								|-
 								|}