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= | [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