Brugia malayi: Difference between revisions

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   good ctg GC%
   good ctg GC%
         #elem  min    max    mean    median  n50   
         #elem  min    max    mean    median  n50   
   all  26878  0.00    72.30  28.86  28.56  29.46
   all  26878  0.00    72.30  '''28.86'''   28.56  29.46
   10K+  1224    24.38  38.44  30.38  30.43  30.62
   10K+  1224    24.38  38.44  '''30.38'''   30.43  30.62


   contaminant ctg len
   contaminant ctg len
         #elem  min    max    mean    median  n50    sum
         #elem  min    max    mean    median  n50    sum
   all  2929    200    8994    740    675    763    2167588
   all  2929    200    8994    740    675    763    '''2167588'''
    
    
   contaminant ctg GC%
   contaminant ctg GC%
         #elem  min    max    mean    median  n50   
         #elem  min    max    mean    median  n50   
   all  2929    18.09  75.96  44.1    43.59  44.80
   all  2929    18.09  75.96  '''44.1'''   43.59  44.80


== Traces ==
== Traces ==

Revision as of 14:21, 19 August 2008

Articles

Genome Info

  • 6 chromosomes: 1-5, XY
  • ~ 90M, 30% GC, 32% coding, 15% repeats

Other sequences

Genome Project

 * 26,879 good ctgs
 * 2,929 contaminants (Example: AAQA01001321 : mouse 99%id hits)
 good ctg len
       #elem   min     max     mean    median  n50     sum
 all   26879   200     611244  3241    1005    19005   87119350
 10K+  1224    10036   611244  41018   23135   60727   50206329
 
 good ctg GC%
       #elem   min     max     mean    median  n50  
 all   26878   0.00    72.30   28.86   28.56   29.46
 10K+  1224    24.38   38.44   30.38   30.43   30.62
 contaminant ctg len
       #elem   min     max     mean    median  n50     sum
 all   2929    200     8994    740     675     763     2167588
 
 contaminant ctg GC%
       #elem   min     max     mean    median  n50  
 all   2929    18.09   75.96   44.1    43.59   44.80

Traces

 Libraries:
   * 2K : bulk of the sequence @TIGR
   * 15-20 K @TIGR
   * 8,000 BAC clones @Children's Hospital Oakland Research Institute.  (!!! no NCBI TA submission)

Trace summary:

  * all:          1,260,215 
  * TRACE_TYPE_CODE 
    * WGS:        1,258,277 
    * TRANSPOSON:     1,437 
    * PRIMER_WALK       501
  * CENTER NAME
    * TIGR:         856,624
    * JCVI          403,591
  * NO BACS !!!; max INSERT_SIZE=23K

Assemblies

TIGR

  • 9X coverage, 856K Sanger traces => 8,200 scaff & 29,808 ctg (avg. scaff=~10K & avg ctg=~3K)
  • "scaffolds totaling ~71 Mb of data with a further ~17.5 Mb of contigs not integrated into any scaffold (orphan contigs)" (Science 2007)

CBCB

Files

/fs/szattic/asmg1/adelcher/Genomes/Brugia : Art's files /fs/szasmg3/dpuiu/Brugia_malayi/