Bacillus anthracis: Difference between revisions
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NC_003997.3 5227293 35.38 Bacillus anthracis str. Ames, complete genome | |||
* not in AA | * not in AA | ||
Revision as of 19:52, 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
NC_003997.3 5227293 35.38 Bacillus anthracis str. Ames, complete genome
- not in AA
AMOScmp-alignmentTrimmed
- no 0 cvg regions when factory trimmed reads aligned to it
- -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:
#elem min max mean median n50 sum snps scf 59 1021 893362 83396 1970 593436 4920387 ctg 67 1021 736364 73430 2483 280568 4919826 496 deg 245 70 141988 2016 671 34515 493924
- There are many stretched mates; no compressed ones !!!
Ctg 0 cvg regions:
#id len gc% start end len cvg ctg7180000001099 2637 35.04 439 2637 2198 0 33.97% gc ; blastn:96% identity to Bacilus cereus ; blastx: alpha/beta hydrolase & protein disulfide isomerase hits ctg7180000001288 28653 36.17 19125 19233 108 0 52.29% gc ; blastn: 100% identity to Ames Ancestor & Sterne ctg7180000001288 28653 36.17 28636 28653 17 0 aligned to other Bacillus anthracis strains ctg7180000001300 156978 35.35 1 161 160 0 46.58% gc ; clonning vector ctg7180000001302 70072 34.28 69464 70072 608 0 55.83% gc ; clonning vector
Deg 0 cvg regions:
all have high GC% (>48.24%) probably cloning vector
Ref breaks:
NC_003997.3 145564 NC_003997.3 627742 NC_003997.3 1151234 NC_003997.3 2085561 NC_003997.3 3515380
Ames Ancestor
- Complete & in AA
NC_007530.2 5227419 35.38 Bacillus anthracis str. 'Ames Ancestor', complete genome NC_007322.2 181677 32.53 Bacillus anthracis str. 'Ames Ancestor' plasmid pXO1, complete sequence NC_007323.3 94830 33.04 Bacillus anthracis str. 'Ames Ancestor' plasmid pXO2, complete sequence
- Downloaded from AA and converted to bank
- Location: /fs/szasmg3/dpuiu/Bacilus_anthracis/AmesAncestor/CS--AI-293
Sterne
- Complete but not in AA.
- NC_005945.1 5228663 bp 35.38% gc
- 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:
#elem min max mean median n50 sum ctg 204 1000 468299 26560 1310 189443 5418252 deg 145 266 32820 1756 804 21949 254596 ctg+deg 349 266 468299 16255 1146 181331 5672848 scf 186 1000 671877 29170 1274 294809 5425585 singleton 2418
Ctg 0 cvg regions:
all have high GC% (>52.08%) probably cloning vector
Deg 0 cvg regions:
#id len gc% deg7180000001258.1-297 297 31.65 deg7180000001300.420-6468 6049 32.05 deg7180000001254.1-28442 28442 33.01 deg7180000001258.557-1060 504 34.52 deg7180000001253.1-576 576 35.76 deg7180000001300.6728-6824 97 36.08 deg7180000001300.1-160 160 38.12 ..
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