Pseudomonas aeruginosa: Difference between revisions

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   [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas%20aeruginosa%20PA14 PA14] [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=CP000438 CP000438] complete : 1 chromosome, 6,537,648 bp, 66.29 %GC
   [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas%20aeruginosa%20PA14 PA14] [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=CP000438 CP000438] complete : 1 chromosome, 6,537,648 bp, 66.29 %GC
    
    
   [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=16720 PA7] [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=150958624
   [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=16720 PA7] [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=CP000744] complete : 1 chromosome, 6588339 bp


=== CBCB ===
=== CBCB ===

Revision as of 21:05, 7 December 2007

Strain PA-b1

Data

NCBI

Related strains

 PAO1 AE004091 complete : 1 chromosome, 6,264,404 bp, 66.56 %GC
 PA14 CP000438 complete : 1 chromosome, 6,537,648 bp, 66.29 %GC
 
 PA7 [1] complete : 1 chromosome, 6588339 bp

CBCB

File location:

 /fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/
 

Files:

 s_1_0001_prb.txt
 s_1_sequence.txt  # contains seq & qual
 s_1_tag.txt         
 s_7_0300_prb.txt
 s_7_sequence.txt  # contains seq & qual
 s_7_tag.txt    
 
 wc -l s_1_sequence.txt s_7_sequence.txt 
  4105993 s_1_sequence.txt
  4521907 s_7_sequence.txt
  8627900 total
 grep -c N s_*seq
  s_1_sequence.seq:37933
  s_7_sequence.seq:69669

Assemblies

CBCB

 1. 2007_1203_AMOSCmp-PAO1
 2. 2007_1203_AMOSCmp-PAO1-relaxed
 3. 2007_1204_AMOSCmp-PA14
 4. 2007_1204_AMOSCmp-PA14-relaxed -> best
 5. 2007_1204_AMOSCmp-PA14-relaxed-noN : removed all reads that contain N's; same parameters as 2007_1204_AMOSCmp-PA14-relaxed => no big differences compared to 2007_1204_AMOSCmp-PA14-relaxed
 QC stats:
 Assembly                              1              2               3              4
 ======================================================================================
 [Info]
 REF                                 PAO1           PAO1           PA14           PA14
 MINCLUSTER                            20             20             20             20
 MINOVL                                10              3             10              3
 MAJORITY                              70             50             70             50
 
 [Scaffolds]
 TotalScaffolds                         1              1              1              1
 TotalContigsInScaffolds             4412           2197           3226           1828
 MeanContigsPerScaffold              4412           2197           3226           1828
 MinContigsPerScaffold               4412           2197           3226           1828
 MaxContigsPerScaffold               4412           2197           3226           1828
 TotalBasesInScaffolds            6000280        5985597        6137031        6127761
 MeanBasesInScaffolds             6000280        5985597        6137031        6127761
 MaxBasesInScaffolds              6000280        5985597        6137031        6127761
 N50ScaffoldBases                 6000280        5985597        6137031        6127761
 TotalSpanOfScaffolds             6264430        6264430        6537674        6537674
 MeanSpanOfScaffolds              6264430        6264430        6537674        6537674
 MinScaffoldSpan                  6264430        6264430        6537674        6537674
 MaxScaffoldSpan                  6264430        6264430        6537674        6537674
 IntraScaffoldGaps                   4411           2196           3225           1827
 2KbScaffolds                           1              1              1              1
 2KbScaffoldSpan                  6264430        6264430        6537674        6537674
 2KbScaffoldPercent                   100            100            100            100
 MeanSequenceGapSize                   59            126            123            223
 
 [Contigs]
 TotalContigs                        4412           2197           3226           1828
 TotalBasesInContigs              6620035        6602214        6791916        6782045
 MeanContigSize                      1500           3005           2105           3710
 MinContigSize                         33             33             33             33
 MaxContigSize                      21576          46268          61425          86811
 N50ContigBases                      3548           8478           6480          14280
 
 [BigContigs_greater_10000]
 TotalBigContigs                       44            173            142            229
 BigContigLength                   547699        2709766        2127747        4558923
 MeanBigContigSize                  12448          15663          14984          19908
 MinBigContig                       10018          10045          10022          10040
 MaxBigContig                       21576          46268          61425          86811
 BigContigsPercentBases                 8             41             31             67
 
 [SmallContigs]
 TotalSmallContigs                   4368           2024           3084           1599
 SmallContigLength                6072336        3892448        4664169        2223122
 MeanSmallContigSize                 1390           1923           1512           1390
 MinSmallContig                        33             33             33             33
 MaxSmallContig                      9964           9996           9977           9995
 SmallContigsPercentBases              92             59             69             33
 
 [Reads]
 TotalReads                       8627900        8627900        8627900        8627900
 ReadsInContigs                   6218126        6218255        6541160        6541364
 BigContigReads                    549658        2601986        2115038        4460608
 SmallContigReads                 5668468        3616269        4426122        2080756
 SingletonReads                   2409774        2409645        2086740        2086536