Table 7.
E. coli dataset
| strain ID | source (GenBank ID) | # of genes | genome length | lab. |
|---|---|---|---|---|
| O26:H11 11368 | AP010953 | 5363(4) | 5697240 | University of Tokyo |
| O157:H7 EC4115 | CP001164 | 5315(0) | 5572075 | J. Craig Venter Institute |
| O157:H7 EDL933 | AE005174 | 5348(10) | 5528445 | University of Wisconsin |
| O157:H7 TW14359 | CP001368 | 5263(6) | 5528136 | University of Washington |
| O157:H7 Sakai | BA000007 | 5360(5) | 5498450 | GIRC |
| O103:H2 12009 | AP010958 | 5053(4) | 5449314 | University of Tokyo |
| O55:H7 CB9615 | CP001846 | 5014(0) | 5386352 | Nankai University |
| O111:H 11128 | AP010960 | 4971(4) | 5371077 | University of Tokyo |
| 042 | FN554766 | 4792(18) | 5241977 | Welcome Trust Sanger Institute |
| CFT073 | AE014075 | 5378(4) | 5231428 | University of Wisconsin |
| ED1a | CU928162 | 4914(4) | 5209548 | Genoscope |
| UMN026 | CU928163 | 4825(4) | 5202090 | Genoscope |
| 55989 | CU928145 | 4762(4) | 5154862 | Institute Pasteur and Genoscope |
| ETEC H10407 | FN649414 | 4696(3) | 5153435 | Welcome Trust Sanger Institute |
| IAI39 | CU928164 | 4731(7) | 5132068 | Genoscope |
| ABU 83972 | CP001671 | 4793(6) | 5131397 | Georg-August-University Goettingen |
| IHE3034 | CP001969 | 4757(3) | 5108383 | IGS |
| APEC O1 | CP000468 | 4467(3) | 5082025 | Iowa State University |
| SMS-3-5 | CP000970 | 4742(3) | 5068389 | TIGR |
| UTI89 | CP000243 | 5066(13) | 5065741 | Washington University |
| S88 | CU928161 | 4695(3) | 5032268 | Genoscope |
| UM146 | CP002167 | 4650(0) | 4993013 | MBRI |
| E24377A | CP000800 | 4755(0) | 4979619 | TIGR |
| O127:H6 E2348/69 | FM180568 | 4553(4) | 4965553 | Sanger Institute |
| 536 | CP000247 | 4629(2) | 4938920 | University of Goettingen |
| W | CP002185 | 4478(4) | 4900968 | AIBN/KRIBB |
| SE11 | AP009240 | 4679(0) | 4887515 | Kitasato Institute for Life Sciences |
| O83:H1 NRG 857C | CP001855 | 4429(13) | 4747819 | Public Health Agency of Canada Laboratory for Foodborne Zoonoses |
| ATCC 8739 | CP000946 | 4180(7) | 4746218 | US DOE Joint Genome Institute |
| SE15 | AP009378 | 4338(0) | 4717338 | Kitasato University |
| IAI1 | CU928160 | 4353(4) | 4700560 | Genoscope |
| K-12 substr. DH10B | CP000948 | 4125(5) | 4686137 | University of Wisconsin-Madison |
| K-12 substr. W3110 | AP009048 | 4225(9) | 4646332 | Nara Institute of Science and Technology |
| HS | CP000802 | 4383(3) | 4643538 | TIGR |
| K-12 substr. MG1655 | U00096 | 4144(7) | 4639675 | University of Wisconsin-Madison |
| DH1 | CP001637 | 4159(4) | 4630707 | US DOE Joint Genome Institute |
| BL21-Gold(DE3)pLysS | CP001665 | 4208(8) | 4629812 | US DOE Joint Genome Institute |
| BW2952 | CP001396 | 4083(5) | 4578159 | TEDA School of Biological Sciences and Biotechnology |
| BL21(DE3) BL21 | AM946981 | 4227(4) | 4570938 | Austrian Center for Biopharmaceutical Technology |
| B REL606 | CP000819 | 4158(6) | 4558953 | International E. coli B Consortium |
| BL21(DE3) | CP001509 | 4181(23) | 4558947 | Korea Research Institute of Bioscience and Biotechnology |
Details for input strains for the E. coli case study. The first number in column called ’# of genes’ corresponds to the number of annotated genes, the second (in brackets) corresponds to the number of genes excluded in the study due to unusual start or stop codons or sequence length not divisible by three.