Bacillus anthracis: Difference between revisions
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== Ames == | == Ames == | ||
* Complete | |||
* not in AA | * not in AA | ||
| Line 77: | Line 78: | ||
Output: | Output: | ||
59 scf | 59 scf | ||
67 ctg | 67 ctg # 496 snps | ||
245 deg | 245 deg | ||
Revision as of 14:05, 16 September 2008
Background
- 89 known strains
- Most virulent: Ames(USA 2001), Vollum (WWII, biological weapon)
- Benign: Sterne (used as vaccine)
- Ames, AmesAncestor, Stern are 99.9% identical; no rearrangements
Genome Projects
Center Complete Assembly Progress Total TIGR/JCVI 2 8 1 11 LANL 0 6 0 6 DOE 1 0 0 1 NMRC 0 0 2 2 Total 3 14 3 20
TIGR/JCVI Strains
Contigs Traces Status Completed Strain 0 96,532 Progress . A0039 62 67,600 Assembly 2007/07/25 Tsiankovskii-I AA ; ??? possible update 1(+2) 101,379 Complete 2004/05/20 Ames Ancestor (Ames 0581) AA ; Insignia 42 86,181 Assembly 2004/06/04 A1055 AA ; Insignia 1(+2) 83,552 Assembly 2005/05/16 A2012 ??? not in Insignia 1 125,879 Complete 2002/05/16 Ames ??? complete but not in AA ; Insignia 49 0 Assembly 2004/06/07 Australia 94 ??? no TRACES ; Insignia 30 90,308 Assembly 2004/06/04 CNEVA-9066 Insignia 64 92,429 Assembly 2004/06/07 Kruger B AA ; Insignia 52 103,144 Assembly 2004/06/04 Vollum Insignia 44 95,078 Assembly 2004/06/07 Western North America USA6153 Insignia
LANL Strains
No traces in TA; none in Insignia
Contigs Traces Status Completed Strain 60 0 Assembly 2008/04/08 A0174 60 0 Assembly 2008/02/12 A0193 68 0 Assembly 2008/03/24 A0389 46 0 Assembly 2008/02/12 A0442 57 0 Assembly 2008/03/24 A0465 63 0 Assembly 2008/01/16 A0488
+ 2 plasmid genome projects (pX01,pX02) completed in 1999
DOE Strains
Contigs Traces Status Completed Strain 1 147,665 Complete 2004/06/24 Sterne ??? complete but not in AA; Insignia
Contigs Traces Status Strain 0 0 Progress 34F2(NMRC) 0 0 Progress 34F2 delta gerH
Strain Assemblies
Ames
- Complete
- not in AA
AMOScmp-alignmentTrimmed
- -D LAYERR=90 => 1 piece
ref=5227293 bp assembly=5227311 amosvalidate=>1555 snps nucmer align of assembly to ref & filter -q => 287 snps
- Many stretched & missoriented mates
- Location: /fs/szasmg3/dpuiu/Bacilus_anthracis/Ames/Assembly/2008_0820_AMOScmp-alignmentTrimmed
CA
Output:
59 scf 67 ctg # 496 snps 245 deg
Ames Ancestor
- Complete & in AA
- Downloaded from AA and converted to bank
- Location: /fs/szasmg3/dpuiu/Bacilus_anthracis/AmesAncestor/CS--AI-293
Sterne
- Complete but not in AA.
- Traces available in TA. Looks like some reads are missing; I'm getting many 0 cvg regions when aligning the reads to the finished genome
#elem min max mean median n50 sum 0cvg 53 8 4946 529 272 1508 28017
AMOScmp
- version: June 12 2007
- untrimmed reads => 358 ctg
- 53 zero cvg regions, max is almost 5K
AMOScmp-alignmentTrimmed
- reads are trimmed according to alignment coords
#elem min max mean median n50 sum ctg 46 736 468060 112792 49000 355370 5188425
CA
- runCA-OBT.pl script
- version 5.1
- Output:
ctg 204 deg 145 scf 186 singleton 2418
Vollum
NCBI data:
#elem min max mean median n50 sum ctg 52 311 812727 105547 29178 400992 5488459
CA
#elem min max mean median n50 sum ctg+deg 57 693 1541457 96154 14641 422289 5480756
ctg 39 1073 1541457 136843 51912 422289 5336858 deg 18 693 54711 7994 2244 54711 143898 scf 25 1440 1593252 214001 94958 676360 5350037