Yersinia pestis
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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
9 Yersinia pestis biovar Antiqua str. B42003004 TIGR 2707 404215 4,841,690 69 72,466 13.0X contigs have many linking mates
10 Yersinia pestis biovar Antiqua str. E1979001 TIGR 2607 360099 4,847,813 75 66,096 11.9X
11 Yersinia pestis biovar Antiqua str. UG05-0454 TIGR 2605 404218 4,838,246 98 72,523 12.3X
12 Yersinia pestis biovar Mediaevalis str. K1973002 TIGR 2618 404216 4,720,694 73 64,204 11.3X
14 Yersinia pestis biovar Orientalis str. F1991016 TIGR 2774 404214 4,892,085 107 65,394 11.6X
15 Yersinia pestis biovar Orientalis str. IP275 TIGR 1019 373665 5,081,206 274 45,934 7.6X
16 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 angola
TIGR Not in AA !! Assembled with CA4, default params /fs/szasmg2/Bacteria/Yersinia_pestis/yersinia_pestis_angola/2007_1128_CA 1 large scaff; many small(<5KB) contigs; some large/deep cvg degen that aligned to related finished plasmids lots of missoriented mates (from all libs); one pile of linking mates; decreasing erate to 0.5% did not generate a better assembly
Yersinia pestis biovar Antiqua str. B42003004
AA:
/fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707 : 69 contigs that have lots of linking mates at the ends
CBCB assembly:
/fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707/2007_1124_CA : sacffolds have lots of missoriented mates 8 scaff, 34 contigs, 1 degen Tried erate=0.5% => no improvement alignment to Yersinia pestis biovar Microtus str. 91001(complete) has many breaks
Yersinia pestis biovar Antiqua str. E1979001
AA:
/fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2607 : 75 contigs that have lots of linking mates at the ends
CBCB assembly:
/fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2607/2007_1128_CA : sacffolds have lots of missoriented mates 8 scaff, 29 contigs, 6 degens Tried erate=0.5% => no improvement
Yersinia pestis biovar Microtus str. 91001 =
China, Not in AA
Name Length %GC Description NC_005810.1 4595065 47.65 Yersinia pestis biovar Microtus str. 91001, complete genome NC_005813.1 70159 44.85 Yersinia pestis biovar Microtus str. 91001 plasmid pCD1, complete sequence NC_005814.1 21742 49.07 Yersinia pestis biovar Microtus str. 91001 plasmid pCRY, complete sequence NC_005815.1 106642 50.31 Yersinia pestis biovar Microtus str. 91001 plasmid pMT1, complete sequence NC_005816.1 9609 45.26 Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence