Ecoli germany: Difference between revisions

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= Close relatives =
= Close relatives =
     NC_011748
     NC_011748   Escherichia coli 55989, complete genome;                             Length: 5,154,862 nt
    Escherichia coli 55989, complete genome
     NC_011752   Escherichia coli 55989 plasmid 55989p, complete sequence;             Length: 72,482 nt
    DNA; circular; Length: 5,154,862 nt
    Replicon Type: chromosome
    Created: 2008/12/16
     NC_011752
    Escherichia coli 55989 plasmid 55989p, complete sequence
    DNA; circular; Length: 72,482 nt
    Replicon Type: plasmid
    Replicon Name: 55989p
    Created: 2008/12/161
 
 
    NC_013353
    Escherichia coli O103:H2 str. 12009, complete genome
    DNA; circular; Length: 5,449,314 nt
    Replicon Type: chromosome
    Created: 2009/10/08
    NC_013354
    Escherichia coli O103:H2 str. 12009 plasmid pO103, complete sequence
    DNA; circular; Length: 75,546 nt
    Replicon Type: plasmid
    Replicon Name: pO103
    Created: 2009/10/07


    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 =
= 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
  ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/
* ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/


= Links =
= Links =
Line 48: Line 27:


   read alignment: CLC; 85% of untrimmed reads aligned
   read alignment: CLC; 85% of untrimmed reads aligned
  6X+ cvg redgions: 490 SNPS s & 1,848 INDELS.   
  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.   
  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.  
  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.   
  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.
   De novo assembly => 3,297 contigs with an N25 of 4K and N50 of 2.5K.


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

Revision as of 13:36, 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