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[[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader. | [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader. | ||
+ | =5= | ||
+ | genomeSize= 6204000 bp | ||
+ | {| {{table}} border="1" | ||
+ | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''All Data''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 1st Set''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 3rd Set''' | ||
+ | |- | ||
+ | |# contigs||[[Media: pbcr_d8_all.fa | 2]]||[[Media: pbcr_d8_rg4_1.fa | 14]]||[[Media: pbcr_d8_rg4_2.fa | 9]]||[[Media: pbcr_d8_rg4_3.fa | 12]] | ||
+ | |- | ||
+ | |Largest contig||5163833||2233593||2243042||2214012 | ||
+ | |- | ||
+ | |Total length|| 5163833||5156868||5169779||5159887 | ||
+ | |- | ||
+ | |N50||5163833||1382073||1271789||13924340 | ||
+ | |- | ||
+ | | style="background:#f0f0f0;"| [[Media:sca_d8.pdf | '''Misassemblies''']]|||||||| | ||
+ | |- | ||
+ | |# misassemblies||1||0||1||0 | ||
+ | |- | ||
+ | |Misassembled contigs length ||5163833||0||2243042||0 | ||
+ | |- | ||
+ | | style="background:#f0f0f0;"| '''Mismatches'''|||||||| | ||
+ | |- | ||
+ | |# mismatches per 100kbp||3.97||8.280||6.93||8.15 | ||
+ | |- | ||
+ | |# indels per 100kbp||0.64||7.33||5.73||5.7 | ||
+ | |- | ||
+ | |# N's per 100kbp ||0||0||0||0 | ||
+ | |- | ||
+ | | style="background:#f0f0f0;"| '''Genome Statistics'''|||||||| | ||
+ | |- | ||
+ | |Genome fraction(%) ||99.945||99.756||99.98||99.775 | ||
+ | |- | ||
+ | |Duplication ratio ||1.001||1||1.002||1.001 | ||
+ | |- | ||
+ | |# genes ||4336 +2 part||4316 +18 part||4331 +8 part||4320 +15 part | ||
+ | |- | ||
+ | |NGA50 ||2926354||1382073||1271789||1392434 | ||
+ | |- | ||
+ | |align="left" style="background:#f0f0f0;"|''' Running Time '''||1hr 19m||41m 3s||32m 30s||31m 16s | ||
+ | |} | ||
+ | [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader. | ||
=Dataset 9 (''E. coli'' K-12, P4-C2 chemistry, 20 Kbp, 1 SMRT cell)= | =Dataset 9 (''E. coli'' K-12, P4-C2 chemistry, 20 Kbp, 1 SMRT cell)= | ||
We used all SMRT cells and evaluated the assemblies by QUAST against the reference genome ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/PBcR_pipeline/D9/report.html more detail]) | We used all SMRT cells and evaluated the assemblies by QUAST against the reference genome ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/PBcR_pipeline/D9/report.html more detail]) |