Yersinia pestis

Data

NCBI

 [16(6)  Genome projects]

Genome projects:

    1  Yersinia pestis Angola [TIGR]                                          !! missing from AA (121 contigs)
    2C Yersinia pestis Antiqua [DOE Joint Genome Institute] complete
    3  Yersinia pestis CA88-4125 [ERIC/Joint Genome Institute, Production
    4C Yersinia pestis CO92 [Sanger Institute] complete
    5  Yersinia pestis FV-1 [TGen]
    6C Yersinia pestis KIM [University of Wisconsin-Madison ...] complete
    7C  Yersinia pestis Nepal516 [DOE Joint Genome Institute] complete
    8C Yersinia pestis Pestoides F [DOE Joint Genome Institute] complete
    9  Yersinia pestis biovar Antiqua str. B42003004 [TIGR]
   10  Yersinia pestis biovar Antiqua str. E1979001 [TIGR]
   11  Yersinia pestis biovar Antiqua str. UG05-0454 [TIGR]
   12  Yersinia pestis biovar Mediaevalis str. K1973002 [TIGR]
   13C Yersinia pestis biovar Microtus str. 91001 [Academy of Military Medical Sciences China] complete
   14  Yersinia pestis biovar Orientalis str. F1991016 [TIGR]
   15  Yersinia pestis biovar Orientalis str. IP275 [TIGR]
   16  Yersinia pestis biovar Orientalis str. MG05-1020 [TIGR]

TA:

   1 yersinia_pestis_angola
   9 yersinia_pestis_biovar_antiqua_str__b42003004
  10 yersinia_pestis_biovar_antiqua_str__e1979001
  11 yersinia_pestis_biovar_antiqua_str__ug05-0454
  12 yersinia_pestis_biovar_mediaevalis_str__k1973002
  14 yersinia_pestis_biovar_orientalis_str__f1991016
  15 yersinia_pestis_biovar_orientalis_str__ip275
  16 yersinia_pestis_biovar_orientalis_str__mg05-1020

AA:

       Assembly Name                                           Subm.   AI      TaxID   Length(bp)      #Ctgs  #Traces  Coverage  Comment
    1  Yersinia pestis biovar Antiqua str. B42003004           TIGR    2707    404215  4,841,690       69      72,466  13.0X     contigs have many linking mates
    2  Yersinia pestis biovar Antiqua str. E1979001            TIGR    2607    360099  4,847,813       75      66,096  11.9X
    3  Yersinia pestis biovar Antiqua str. UG05-0454           TIGR    2605    404218  4,838,246       98      72,523  12.3X
    4  Yersinia pestis biovar Mediaevalis str. K1973002        TIGR    2618    404216  4,720,694       73      64,204  11.3X
    5  Yersinia pestis biovar Orientalis str. F1991016         TIGR    2774    404214  4,892,085       107     65,394  11.6X
    6  Yersinia pestis biovar Orientalis str. IP275            TIGR    1019    373665  5,081,206       274     45,934  7.6X
    7  Yersinia pestis biovar Orientalis str. MG05-1020        TIGR    2608    404217  4,977,609       80      71,897  12.1X

DOE

 Microbial Genomes (assembly seq, no traces)

Sanger

 Genome project (assembly seq, no traces)

Assemblies

Yersinia pestis biovar Antiqua str. B42003004

AA:

 /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707 : contigs have lots of linking mates

CBCB assembly:

 /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707/2007_1124_CA : sacffolds have lots of missoriented mates
 8 scaff, 34 contigs, 1degen

 Tried erate=0.5% => no improvement
 alignment to Yersinia pestis biovar Microtus str. 91001(complete) has many breaks