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* '''Evaluated by QUAST''' |
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* '''Evaluated by QUAST''' |
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: [http://bioinf.spbau.ru/en/quast/ QUAST] (QUAST v2.2)
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: [http://bioinf.spbau.ru/en/quast/ QUAST] (QUAST v2.3)
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: Running QUAST requires [[Media: Ec_gene_result.ncbi | Ec_gene_list]] and [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913.fna]. There are 4497 genes in total. |
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: Running QUAST requires [[Media: Ec_gene_result.ncbi | Ec_gene_list]] and [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913.fna]. There are 4497 genes in total. |
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*'''Score with QUAST: With PacBio Long Reads''' [http://sb.nhri.org.tw/comps/quast/Allpaths-LG/E_coli/report.html more detail] |
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*'''Score with QUAST: With PacBio Long Reads''' [http://sb.nhri.org.tw/comps/quast/Allpaths-LG/E_coli/report.html more detail] |
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| # contigs||[[Media:alg_d1_web.fasta | 1]]||[[Media:alg_d1_raw.fasta | 14]]||[[Media:alg_d1_frac.fasta | 1]]||[[Media:alg_d1_50X.fasta | 1]]||[[Media:alg_d1_100X.fasta | 1]]
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| # contigs||[[Media:spd_d1_web.fasta | 1]]||[[Media:spd_d1_raw.fasta | 14]]
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| Largest contig||4638970||4625005||4638970||4638970||4638970
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| Largest contig||4638970||4625005
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| Total length||4638970||4652215||4638970||4638970||4638970
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| Total length||4638970||4652215
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| N50||4638970||4625005||4638970||4638970||4638970
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| N50||4638970||4625005
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| align="left" style="background:#f0f0f0;"|[[Media: allpaths_d1.pdf | '''Misassemblies''']] |
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| align="left" style="background:#f0f0f0;"|[[Media: allpaths_d1.pdf | '''Misassemblies''']] |
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| # misassemblies||1||5||1||1||1
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| # misassemblies||1||5
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|Misassembled contigs length ||4638970||4625005||4638970||4638970||4638970
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|Misassembled contigs length ||4638970||4625005
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| align="left" style="background:#f0f0f0;"|'''Mismatches''' |
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| align="left" style="background:#f0f0f0;"|'''Mismatches''' |
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|# mismatches per 100kbp ||0.11||1.06||0.06||0.09||0.06
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|# mismatches per 100kbp ||0.11||1.06
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|# indels per 100kbp ||0.09||0.61||0.09||0.09||0.09
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|# indels per 100kbp ||0.09||0.61
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|# N's per 100kbp ||0||282.94||0||0.04||0
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|# N's per 100kbp ||0||282.94
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| align="left" style="background:#f0f0f0;"|'''Genome statistics''' |
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| align="left" style="background:#f0f0f0;"|'''Genome statistics''' |
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| Genome fraction (%)||99.983||99.418||99.983||99.983||99.983
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| Genome fraction (%)||99.983||99.418
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| Duplication ratio ||1||1.013||1||1||1
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| Duplication ratio ||1||1.013
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| # genes||4494 + 1 part||4471 + 2 part ||4494 + 1 part　||4494 + 1 part||4494 + 1 part
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| # genes||4494 + 1 part||4471 + 2 part t
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| NGA50 || 4638970 || 2714032 || 3763133 || 4209920 || 3762305
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| NGA50 || 4638970 || 2714032
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| align="left" style="background:#f0f0f0;"|''' Running Time '''|| 42m ||2hr 35m||35m ||35m || 41m
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| align="left" style="background:#f0f0f0;"|''' Running Time '''|| 42m ||2hr 35m
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