Criteria for scoring prophage regions (as intact, questionable, or incomplete): Method 1: 1. If the number of certain phage organism in this table is more than or equal to 100% of the total number of CDS of the region, the region is marked with total score 150. If less than 100%, method 2 and 3 will be used. Method 2: 1. If the number of certain phage organism in this table is more than 50% of the total number of CDS of the region, that phage organism is considered as the major potential phage for that region; the percentage of the total number of that phage organism in this table in the total number of proteins of the region is calculated and then multipled by 100; the percentage of the length of that phage organism in this table in the length of the region is calculated and then multipled by 50 (phage head's encapsulation capability is considered). Method 3: 1. If any of the specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin') are present, the score will be increased by 10 for each keyword found. 2. If the size of the region is greater than 30 Kb, the score will be increased by 10. 3. If there are at least 40 proteins in the region, the score will be increased by 10. 4. If all of the phage-related proteins and hypothetical proteins constitute more than 70% of the total number of proteins in the region, the score will be increased by 10. Compared the total score of method 2 with the total score of method 3, the bigger one is chosen as the total score of the region. If the region's total score is less than 70, it is marked as incomplete; if between 70 to 90, it is marked as questionable; if greater than 90, it is marked as intact. Totally 10 intact prophage regions have been identified. gi|188491671|ref|AAKB00000000.2| Escherichia coli 53638 , whole genome shotgun .5071018, gc%: 51.10% REGION REGION_LENGTH COMPLETENESS(score) SPECIFIC_KEYWORD REGION_POSITION TRNA_NUM TOTAL_PROTEIN_NUM PHAGE_HIT_PROTEIN_NUM HYPOTHETICAL_PROTEIN_NUM PHAGE+HYPO_PROTEIN_PERCENTAGE BACTERIAL_PROTEIN_NUM ATT_SITE_SHOWUP PHAGE_SPECIES_NUM MOST_COMMON_PHAGE_NAME MOST_COMMON_PHAGE_NUM MOST_COMMON_PHAGE_PERCENTAGE GC_PERCENTAGE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1 7.6Kb incomplete(60) transposase,lysis 34-7698 4 12 10 1 91.6% 1 no 7 PHAGE_Stx2_c_1717 4 33.3% 50.23% 2 20.7Kb incomplete(30) transposase,integrase 8573-29316 0 11 9 0 81.8% 2 yes 8 PHAGE_Gifsy_2 2 18.1% 48.13% 3 68.5Kb intact(150) tail,head,capsid,portal,terminase,lysin,integrase 44403-112951 0 55 45 2 85.4% 8 yes 18 PHAGE_Entero_mEp460 19 34.5% 51.16% 4 35.8Kb questionable(70) protease,head,capsid,integrase 362913-398750 1 27 13 7 74% 7 yes 11 PHAGE_Gifsy_1 2 7.4% 51.20% 5 9.8Kb intact(107) transposase,head 949585-959433 0 14 13 1 100% 0 no 2 PHAGE_Entero_P4 10 71.4% 55.17% 6 37.7Kb intact(96) tail 1121698-1159430 0 53 43 6 92.4% 4 no 8 PHAGE_Burkho_BcepMu 34 64.1% 54.38% 7 36.5Kb intact(123) lysis 1832647-1869235 0 46 40 3 93.4% 3 yes 5 PHAGE_Yersin_413C 33 71.7% 51.98% 8 12Kb incomplete(60) transposase 2038959-2050998 0 11 10 0 90.9% 1 no 7 PROPHAGE_Escher_MG1655 3 27.2% 51.58% 9 9.1Kb incomplete(30) tail,transposase 3212914-3222068 0 10 7 0 70% 3 no 7 PHAGE_Entero_phiEF24C 1 10% 50.09% 10 29.2Kb intact(110) lysin,lysis,terminase,virion,plate,tail,transposase 3328202-3357442 0 36 32 1 91.6% 3 no 13 PHAGE_Burkho_Bcep43 13 36.1% 51.59% 11 62.6Kb intact(150) integrase,transposase,lysis,terminase,head,capsid,tail,plate 3700803-3763449 4 73 52 6 79.4% 15 yes 33 PHAGE_Aggreg_S1249 9 12.3% 50.09% 12 34.2Kb intact(100) protease,lysin,transposase,terminase,tail 3905690-3939953 4 49 41 3 89.7% 5 no 18 PHAGE_Entero_phiP27 17 34.6% 48.95% 13 10.1Kb incomplete(60) transposase,capsid,head 3950721-3960897 0 14 7 4 78.5% 3 no 5 PHAGE_Gifsy_1 2 14.2% 50.41% 14 72.9Kb intact(150) transposase,tail,lysis,head,portal,virion,protease,plate,terminase,capsid,integrase 4192498-4265416 0 99 80 12 92.9% 7 yes 15 PHAGE_Entero_Mu 49 49.4% 51.89% 15 48.9Kb intact(150) integrase,protease,transposase,lysin,lysis,terminase,head,portal,capsid,tail 4303022-4351984 4 65 52 8 92.3% 5 yes 12 PHAGE_Entero_mEp460 20 30.7% 51.26% 16 14.2Kb intact(110) tail,plate,terminase,transposase 5056750-5071018 0 19 15 3 94.7% 1 no 7 PHAGE_Entero_4795 4 21% 50.42%