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 4 intact prophage regions have been identified. gi|00000000|ref|NC_000000| Salmonella enterica subsp. enterica serovar Dublin strain 5001303, gc%: 52.09% REGION REGION_LENGTH COMPLETENESS(score) SPECIFIC_KEYWORD REGION_POSITION RNA_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(hit_genes_count) FIRST_MOST_COMMON_PHAGE_NUM FIRST_MOST_COMMON_PHAGE_PERCENTAGE GC_PERCENTAGE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1 8.3Kb incomplete(60) transposase,tail,plate 773879-782230 0 12 8 3 91.6% 1 no 6 PHAGE_Phage_Gifsy_2_NC_010393(3),PHAGE_Salmon_RE_2010_NC_019488(2),PHAGE_Salmon_Fels_1_NC_010391(2),PHAGE_Escher_SH2026Stx1_NC_049919(1),PHAGE_Entero_HK140_NC_019710(1),PHAGE_Stx2_c_1717_NC_011357(1),PHAGE_Salmon_SEN4_NC_029015(1),PHAGE_Erwini_vB_EhrS_49_NC_048197(1),PHAGE_Escher_vB_EcoM_4HA13_NC_049466(1),PHAGE_Salmon_SEN8_NC_047753(1),PHAGE_Entero_mEp237_NC_019704(1),PHAGE_Erwini_vB_EhrS_59_NC_048198(1),PHAGE_Salmon_Fels_2_NC_010463(1),PHAGE_Entero_mEp390_NC_019721(1),PHAGE_Vibrio_CP_T1_NC_019457(1),PHAGE_Vibrio_vB_VchM_138_NC_019518(1),PHAGE_Salmon_SI7_NC_049460(1),PHAGE_Stx2_c_Stx2a_F451_NC_049924(1),PHAGE_Phage_Gifsy_1_NC_010392(1),PHAGE_Salmon_SEN5_NC_028701(1),PHAGE_Pseudo_F116_NC_006552(1),PHAGE_Salmon_SJ46_NC_031129(1),PHAGE_Entero_phi80_NC_021190(1),PHAGE_Stenot_Smp131_NC_023588(1),PHAGE_Stenot_S1_NC_011589(1),PHAGE_Entero_HK225_NC_019717(1) 3 25% 46.05% 2 25Kb incomplete(50) terminase,tail,integrase 794194-819282 0 31 28 2 96.7% 1 yes 14 PHAGE_Phage_Gifsy_2_NC_010393(18),PHAGE_Salmon_SPN3UB_NC_019545(15),PHAGE_Phage_Gifsy_1_NC_010392(15),PHAGE_Salmon_SEN34_NC_028699(11),PHAGE_Entero_mEp237_NC_019704(8),PHAGE_Salmon_BTP1_NC_042346(4),PHAGE_Entero_YYZ_2008_NC_011356(3),PHAGE_Salmon_Fels_1_NC_010391(3),PHAGE_Entero_HK225_NC_019717(2),PHAGE_Entero_BP_4795_NC_004813(2),PHAGE_Entero_phi80_NC_021190(2),PHAGE_Entero_phiP27_NC_003356(2),PHAGE_Salmon_ST64T_NC_004348(2),PHAGE_Salmon_vB_SemP_Emek_NC_018275(2),PHAGE_Salmon_118970_sal3_NC_031940(2),PHAGE_Salmon_ST64B_NC_004313(2),PHAGE_Pectob_ZF40_NC_019522(1),PHAGE_Mycoba_Gumball_NC_011290(1),PHAGE_Entero_mEpX1_NC_019709(1),PHAGE_Burkho_BcepB1A_NC_005886(1),PHAGE_Shigel_POCJ13_NC_025434(1),PHAGE_Burkho_BcepNY3_NC_009604(1),PHAGE_Gordon_Nymphadora_NC_031061(1),PHAGE_Serrat_Parlo_NC_048758(1),PHAGE_Burkho_Bcep1_NC_005263(1),PHAGE_Shigel_Stx_NC_029120(1),PHAGE_Entero_SfV_NC_003444(1),PHAGE_Salmon_SSU5_NC_018843(1),PHAGE_Rhizob_RHEph10_NC_034248(1),PHAGE_Burkho_BcepC6B_NC_005887(1),PHAGE_Pectob_DU_PP_V_NC_047887(1),PHAGE_Pseudo_F116_NC_006552(1),PHAGE_Salmon_SEN5_NC_028701(1),PHAGE_Burkho_Bcep781_NC_004333(1),PHAGE_Shigel_SfIV_NC_022749(1),PHAGE_Entero_Arya_NC_031048(1),PHAGE_Cronob_phiES15_NC_018454(1),PHAGE_Salmon_SEN4_NC_029015(1),PHAGE_Pseudo_nickie_NC_042091(1),PHAGE_Erwini_vB_EhrS_49_NC_048197(1),PHAGE_Burkho_BcepMigl_NC_019917(1),PHAGE_Lister_A118_NC_003216(1),PHAGE_Burkho_Bcep43_NC_005342(1),PHAGE_Agroba_Atu_ph07_NC_042013(1),PHAGE_Burkho_Bcep22_NC_005262(1),PHAGE_Shigel_SfII_NC_021857(1) 10 58.06% 51.49% 3 16.5Kb questionable(80) recombinase,tail,terminase,lysin,integrase 1443344-1459925 0 12 9 1 83.3% 2 yes 7 PHAGE_Salmon_Fels_1_NC_010391(4),PHAGE_Phage_Gifsy_2_NC_010393(3),PHAGE_Phage_Gifsy_1_NC_010392(3),PHAGE_Salmon_ST64B_NC_004313(2),PHAGE_Salmon_SPN1S_NC_016761(2),PHAGE_Salmon_BPS17W1_NC_042097(1),PHAGE_Entero_mEp390_NC_019721(1),PHAGE_Entero_HK97_NC_002167(1),PHAGE_Escher_Skarpretter_NC_048112(1),PHAGE_Entero_HK106_NC_019768(1),PHAGE_Entero_Tyrion_NC_031077(1),PHAGE_Salmon_SI7_NC_049460(1),PHAGE_Entero_mEp235_NC_019708(1),PHAGE_Escher_500465_1_NC_049342(1),PHAGE_Entero_lambda_NC_001416(1),PHAGE_Entero_HK022_NC_002166(1),PHAGE_Escher_C130_2_NC_048067(1),PHAGE_Salmon_RE_2010_NC_019488(1),PHAGE_Erwini_phiEt88_NC_015295(1),PHAGE_Entero_mEp213_NC_019720(1),PHAGE_Salmon_epsilon15_NC_004775(1),PHAGE_Entero_c_1_NC_019706(1),PHAGE_Salmon_SEN5_NC_028701(1),PHAGE_Escher_TL_2011b_NC_019445(1),PHAGE_Salmon_SJ46_NC_031129(1),PHAGE_Entero_IME_EC2_NC_047742(1),PHAGE_Entero_N15_NC_001901(1) 2 33.33% 44.61% 4 44.6Kb intact(120) tail,injection,head,capsid,portal,integrase 2267304-2311988 0 62 61 1 100% 0 yes 21 PHAGE_Salmon_ST160_NC_014900(26),PHAGE_Entero_UAB_Phi20_NC_031019(22),PHAGE_Salmon_epsilon34_NC_011976(19),PHAGE_Salmon_SE1_NC_011802(18),PHAGE_Salmon_BTP1_NC_042346(16),PHAGE_Salmon_g341c_NC_013059(15),PHAGE_Salmon_ST64T_NC_004348(14),PHAGE_Entero_ST104_NC_005841(13),PHAGE_Salmon_UPF_BP1_NC_047875(11),PHAGE_Salmon_118970_sal4_NC_030919(11),PHAGE_Salmon_vB_SemP_Emek_NC_018275(10),PHAGE_Salmon_SEN22_NC_028696(8),PHAGE_Salmon_103203_sal5_NC_031946(8),PHAGE_Entero_P22_NC_002371(7),PHAGE_Entero_ES18_NC_006949(7),PHAGE_Salmon_SPN9CC_NC_017985(5),PHAGE_Salmon_vB_SosS_Oslo_NC_018279(4),PHAGE_Entero_mEp235_NC_019708(3),PHAGE_Entero_Sf101_NC_027398(3),PHAGE_Shigel_Sf6_NC_005344(3),PHAGE_Entero_c_1_NC_019706(3),PHAGE_Entero_SfI_NC_027339(2),PHAGE_Entero_mEp234_NC_019715(2),PHAGE_Entero_VT2_Sakai_NC_000902(2),PHAGE_Salmon_HK620_NC_002730(2),PHAGE_Entero_mEpX2_NC_019705(2),PHAGE_Entero_HK022_NC_002166(2),PHAGE_Entero_933W_NC_000924(2),PHAGE_Escher_HK639_NC_016158(2),PHAGE_Stx2_II_NC_004914(2),PHAGE_Entero_mEp460_NC_019716(1),PHAGE_Stx2_c_Stx2a_F451_NC_049924(1),PHAGE_Salmon_SPN3UB_NC_019545(1),PHAGE_Stx2_c_1717_NC_011357(1),PHAGE_Erwini_vB_EhrS_59_NC_048198(1),PHAGE_Shigel_Stx_NC_029120(1),PHAGE_Entero_Min27_NC_010237(1),PHAGE_Entero_DE3_NC_042057(1),PHAGE_Escher_phage_NC_004913(1),PHAGE_Entero_HK446_NC_019714(1),PHAGE_Klebsi_phiKO2_NC_005857(1),PHAGE_Shigel_POCJ13_NC_025434(1),PHAGE_Entero_HK225_NC_019717(1),PHAGE_Escher_Lys12581Vzw_NC_049917(1),PHAGE_Bacter_APSE_2_NC_011551(1),PHAGE_Entero_N15_NC_001901(1),PHAGE_Salmon_ST64B_NC_004313(1),PHAGE_Escher_HK75_NC_016160(1),PHAGE_Entero_HK633_NC_019719(1),PHAGE_Salmon_SEN34_NC_028699(1),PHAGE_Entero_HK106_NC_019768(1),PHAGE_Escher_SH2026Stx1_NC_049919(1),PHAGE_Stx2_c_Stx2a_WGPS9_NC_049923(1),PHAGE_Entero_lambda_NC_001416(1),PHAGE_Entero_VT2phi_272_NC_028656(1),PHAGE_Escher_phiV10_NC_007804(1),PHAGE_Entero_mEp213_NC_019720(1),PHAGE_Escher_RCS47_NC_042128(1),PHAGE_Stx2_c_86_NC_008464(1),PHAGE_Salmon_epsilon15_NC_004775(1),PHAGE_Salmon_SJ46_NC_031129(1),PHAGE_Escher_ArgO145_NC_049918(1) 10 41.93% 47.11% 5 52.7Kb intact(150) transposase,recombinase,tail,plate,capsid,head,terminase,lysin,integrase 2631979-2684695 0 65 58 6 98.4% 1 yes 13 PHAGE_Salmon_118970_sal3_NC_031940(66),PHAGE_Salmon_ST64B_NC_004313(40),PHAGE_Shigel_SfII_NC_021857(12),PHAGE_Entero_SfV_NC_003444(10),PHAGE_Shigel_SfIV_NC_022749(10),PHAGE_Entero_SfI_NC_027339(8),PHAGE_Entero_phiP27_NC_003356(6),PHAGE_Entero_mEp460_NC_019716(6),PHAGE_Entero_cdtI_NC_009514(3),PHAGE_Salmon_SJ46_NC_031129(3),PHAGE_Salmon_vB_SemP_Emek_NC_018275(2),PHAGE_Escher_500465_1_NC_049342(1),PHAGE_Lister_A118_NC_003216(1),PHAGE_Clostr_phiMMP02_NC_019421(1),PHAGE_Salmon_ST64T_NC_004348(1),PHAGE_Gordon_Nymphadora_NC_031061(1),PHAGE_Erwini_vB_EhrS_49_NC_048197(1),PHAGE_Vibrio_X29_NC_024369(1),PHAGE_Stx2_c_Stx2a_WGPS9_NC_049923(1),PHAGE_Salmon_SEN22_NC_028696(1),PHAGE_Entero_mEp390_NC_019721(1),PHAGE_Entero_P1_NC_005856(1),PHAGE_Clostr_CDKM9_NC_048642(1),PHAGE_Salmon_SPN3UB_NC_019545(1),PHAGE_Escher_500465_2_NC_049343(1),PHAGE_Salmon_SEN34_NC_028699(1),PHAGE_Entero_HK106_NC_019768(1),PHAGE_Entero_HK633_NC_019719(1),PHAGE_Entero_EFC_1_NC_025453(1),PHAGE_Pectob_ZF40_NC_019522(1),PHAGE_Clostr_phiCTP1_NC_014457(1),PHAGE_Clostr_phiC2_NC_009231(1),PHAGE_Thermu_OH2_NC_021784(1),PHAGE_Escher_pro483_NC_028943(1),PHAGE_Clostr_phiMMP03_NC_028959(1),PHAGE_Salmon_g341c_NC_013059(1),PHAGE_Salmon_Fels_1_NC_010391(1),PHAGE_Entero_933W_NC_000924(1),PHAGE_Stx2_vB_EcoP_24B_NC_027984(1) 22 101.53% 48.44% 6 42.9Kb intact(150) tail,plate,lysis,head,terminase,capsid,portal,integrase,transposase 4151909-4194884 0 51 45 6 100% 0 yes 14 PHAGE_Salmon_SEN8_NC_047753(29),PHAGE_Salmon_Fels_2_NC_010463(27),PHAGE_Salmon_RE_2010_NC_019488(26),PHAGE_Escher_500465_1_NC_049342(23),PHAGE_Klebsi_4LV2017_NC_047818(22),PHAGE_Klebsi_ST512_KPC3phi13.2_NC_049452(15),PHAGE_Klebsi_ST437_OXA245phi4.2_NC_049449(15),PHAGE_Klebsi_ST437_OXA245phi4.1_NC_049448(10),PHAGE_Klebsi_ST15_OXA48phi14.1_NC_049454(7),PHAGE_Klebsi_ST13_OXA48phi12.1_NC_049453(7),PHAGE_Entero_RB49_NC_005066(1),PHAGE_Hypert_2_NC_014321(1),PHAGE_Bacill_SPbeta_NC_001884(1),PHAGE_Sulfol_SMV1_NC_023585(1),PHAGE_Entero_GEC_3S_NC_025425(1),PHAGE_Bacill_G_NC_023719(1),PHAGE_Plankt_PaV_LD_NC_016564(1),PHAGE_Salmon_SJ46_NC_031129(1),PHAGE_Salmon_118970_sal3_NC_031940(1),PHAGE_Salmon_ST64B_NC_004313(1),PHAGE_Entero_P1_NC_005856(1),PHAGE_Flavob_vB_FspS_laban6_1_NC_048834(1),PHAGE_Cronob_ESSI_2_NC_047854(1),PHAGE_Lactob_CL1_NC_028888(1),PHAGE_Klebsi_ST16_OXA48phi5.4_NC_049450(1),PHAGE_Mannhe_phiMHaA1_NC_008201(1) 12 56.86% 51.44% 7 45.5Kb intact(150) tail,protease,portal,terminase,lysis,integrase 4674172-4719702 0 55 44 7 92.7% 4 yes 16 PHAGE_Phage_Gifsy_2_NC_010393(32),PHAGE_Salmon_Fels_1_NC_010391(19),PHAGE_Phage_Gifsy_1_NC_010392(15),PHAGE_Entero_mEp460_NC_019716(12),PHAGE_Entero_cdtI_NC_009514(12),PHAGE_Entero_c_1_NC_019706(8),PHAGE_Entero_mEp213_NC_019720(7),PHAGE_Salmon_SEN34_NC_028699(6),PHAGE_Entero_mEp237_NC_019704(5),PHAGE_Entero_DE3_NC_042057(4),PHAGE_Entero_HK225_NC_019717(4),PHAGE_Entero_lambda_NC_001416(4),PHAGE_Salmon_SPN3UB_NC_019545(3),PHAGE_Cronob_phiES15_NC_018454(3),PHAGE_Entero_HK630_NC_019723(3),PHAGE_Salmon_RE_2010_NC_019488(2),PHAGE_Entero_mEpX1_NC_019709(2),PHAGE_Edward_GF_2_NC_026611(2),PHAGE_Entero_phi80_NC_021190(2),PHAGE_Salmon_epsilon15_NC_004775(2),PHAGE_Salmon_SEN5_NC_028701(2),PHAGE_Escher_TL_2011b_NC_019445(2),PHAGE_Salmon_SPN1S_NC_016761(2),PHAGE_Entero_Tyrion_NC_031077(2),PHAGE_Salmon_SEN4_NC_029015(2),PHAGE_Erwini_phiEt88_NC_015295(1),PHAGE_Escher_ECP1_NC_049926(1),PHAGE_Klebsi_phiKO2_NC_005857(1),PHAGE_Shigel_POCJ13_NC_025434(1),PHAGE_Bacill_G_NC_023719(1),PHAGE_Escher_pro483_NC_028943(1),PHAGE_Escher_Lys12581Vzw_NC_049917(1),PHAGE_Thermu_OH2_NC_021784(1),PHAGE_Entero_N15_NC_001901(1),PHAGE_Pseudo_MP1412_NC_018282(1),PHAGE_Burkho_vB_BmuP_KL4_NC_047958(1),PHAGE_Entero_HK629_NC_019711(1),PHAGE_Entero_YYZ_2008_NC_011356(1),PHAGE_Entero_Mu_NC_000929(1),PHAGE_Bacill_1_NC_009737(1),PHAGE_Entero_mEp235_NC_019708(1),PHAGE_Salmon_Fels_2_NC_010463(1),PHAGE_Shigel_Stx_NC_029120(1),PHAGE_Entero_HK022_NC_002166(1),PHAGE_Escher_phiV10_NC_007804(1),PHAGE_Pseudo_MD8_NC_031091(1),PHAGE_Escher_HK639_NC_016158(1),PHAGE_Yersin_PY54_NC_005069(1),PHAGE_Bacill_SP_15_NC_031245(1),PHAGE_Entero_ES18_NC_006949(1),PHAGE_Mannhe_vB_MhS_1152AP2_NC_028956(1),PHAGE_Salmon_SJ46_NC_031129(1),PHAGE_Salmon_ST64B_NC_004313(1),PHAGE_Geobac_GBSV1_NC_008376(1),PHAGE_Entero_HK97_NC_002167(1),PHAGE_Entero_HK106_NC_019768(1),PHAGE_Salmon_SI7_NC_049460(1),PHAGE_Klebsi_ST16_OXA48phi5.4_NC_049450(1),PHAGE_Entero_vB_EcoM_VR25_NC_028925(1),PHAGE_Escher_500465_1_NC_049342(1),PHAGE_Salmon_SEN8_NC_047753(1) 28 58.18% 50.97%