Ecoli germany: Difference between revisions

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= Data =
= Data =
* http://www.genomics.cn/en/news_show.php?type=show&id=644
* [http://www.genomics.cn/en/news_show.php?type=show&id=644 BGI Sequences Genome of the Deadly E. Coli in Germany and Reveals New Super-Toxic Strain June 2nd 2011]
* ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/
* [ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/ BGI run1-7 & assembly]


= Links =
= Links =

Revision as of 13:39, 5 June 2011

Close relatives

   NC_011748	   Escherichia coli 55989, complete genome;                              Length: 5,154,862 nt
   NC_011752	   Escherichia coli 55989 plasmid 55989p, complete sequence;             Length: 72,482 nt
   NC_013353	   Escherichia coli O103:H2 str. 12009, complete genome;                 Length: 5,449,314 nt
   NC_013354	   Escherichia coli O103:H2 str. 12009 plasmid pO103, complete sequence; Length: 75,546 nt

Data

Links

Assemblies

EdgeBio CLC & newbler

 read QC: FastQC 
 read trimming: CLC
 .                    elem       min    q1     q2     q3     max        mean       n50        sum          
 run                  629368     5      99     106    109    135        102        107        63944436 
 run.trimmed          617257     10     46     69     86     94         64         79         39745910   
 read alignment: CLC; 85% of untrimmed reads aligned
 6X+ cvg regions: 490 SNPS s & 1,848 INDELS.  
 De novo assembly of 90K reads that did not map, 58K assembled together => 363 contigs ranging in size from 400 to 7800 bp.  
 Contigs were blasted against NRNT at NCBI with a minimum .01 e-value. 
 Hits:  E. coli strains (such as O83:H1 and O42) , Shigella flexneri, Salmonella, and Cronobacter.  
 De novo assembly => 3,297 contigs with an N25 of 4K and N50 of 2.5K.

Assembly stats

 .                         elem       min    q1     q2     q3     max        mean       n50        sum            
 CA.ctg+deg                22395      64     107    159    253    2367       204        216        4567575        
 newbler.Ecoli_55989.ctg   8357       100    218    397    696    5038       534        639        4465330
 AMOScmp.Ecoli_55989.ctg   1321       65     425    1780   5257   40345      3774       7775       4985978