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 Paratyphi C strain 4775967, gc%: 52.17%
                                  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              30.7Kb                   intact(150)                   recombinase,portal,terminase,capsid,head,tail,plate     contig,9,at,799234:107296-138017            0                        37                      36                               1                                100%                             0                                yes                              12                               PHAGE_Cronob_ESSI_2_NC_047854(27),PHAGE_Salmon_SI7_NC_049460(19),PHAGE_Haemop_HP2_NC_003315(12),PHAGE_Aeromo_phiO18P_NC_009542(12),PHAGE_Haemop_HP1_NC_001697(12),PHAGE_Pasteu_F108_NC_008193(5),PHAGE_Klebsi_4LV2017_NC_047818(4),PHAGE_Klebsi_ST437_OXA245phi4.2_NC_049449(4),PHAGE_Salmon_SW9_NC_049459(4),PHAGE_Vibrio_1.202.O._10N.222.45.E8_NC_048066(4),PHAGE_Salmon_Fels_2_NC_010463(3),PHAGE_Vibrio_K139_NC_003313(3),PHAGE_Salini_SMHB1_NC_047775(3),PHAGE_Salmon_SEN1_NC_029003(2),PHAGE_Pseudo_C5a_NC_047790(2),PHAGE_Entero_PsP3_NC_005340(2),PHAGE_Klebsi_ST512_KPC3phi13.2_NC_049452(2),PHAGE_Salmon_SP_004_NC_021774(2),PHAGE_Vibrio_PV94_NC_027368(2),PHAGE_Vibrio_8_NC_022747(2),PHAGE_Salmon_SEN8_NC_047753(2),PHAGE_Klebsi_ST13_OXA48phi12.1_NC_049453(2),PHAGE_Salmon_RE_2010_NC_019488(2),PHAGE_Pseudo_phi3_NC_030940(2),PHAGE_Vibrio_Valm_yong1_NC_049477(2),PHAGE_Klebsi_ST15_OXA48phi14.1_NC_049454(2),PHAGE_Salmon_118970_sal3_NC_031940(1),PHAGE_Erwini_EtG_NC_047833(1),PHAGE_Aggreg_S1249_NC_013597(1),PHAGE_Escher_pro483_NC_028943(1),PHAGE_Entero_Phieco32_NC_010324(1),PHAGE_Salmon_vB_SenS_Sasha_NC_047786(1),PHAGE_Erwini_phiEa21_4_NC_011811(1),PHAGE_Salmon_SEN4_NC_029015(1),PHAGE_Pseudo_119X_NC_007807(1),PHAGE_Aeromo_pAh6_C_NC_025459(1),PHAGE_Pseudo_PaP2_NC_005884(1),PHAGE_Phage_vB_EcoP_SU10_NC_027395(1),PHAGE_Klebsi_ST147_VIM1phi7.1_NC_049451(1),PHAGE_Erwini_vB_Eam_MM7_NC_041978(1),PHAGE_Burkho_KS9_NC_013055(1),PHAGE_Klebsi_ST437_OXA245phi4.1_NC_049448(1),PHAGE_Salmon_SEN5_NC_028701(1),PHAGE_Entero_phiT5282H_NC_049429(1),PHAGE_Entero_NJ01_NC_018835(1),PHAGE_Erwini_ENT90_NC_019932(1),PHAGE_Mycoba_Thyatira_NC_051597(1),PHAGE_Erwini_phiEa104_NC_015292(1),PHAGE_Escher_520873_NC_049344(1)   23                               72.97%                           50.21%                        
                                  2              26Kb                     intact(140)                   lysis,terminase,portal,head,capsid,tail,plate     contig,14,at,1065241:1-26086          0                        35                      34                               0                                97.1%                            1                                no                               12                               PHAGE_Salmon_SEN34_NC_028699(26),PHAGE_Psychr_pOW20_A_NC_020841(6),PHAGE_Haemop_Aaphi23_NC_004827(5),PHAGE_Aggreg_S1249_NC_013597(4),PHAGE_Vibrio_CP_T1_NC_019457(3),PHAGE_Salmon_Fels_2_NC_010463(3),PHAGE_Edward_GF_2_NC_026611(3),PHAGE_Salmon_vB_SosS_Oslo_NC_018279(2),PHAGE_Pantoe_vB_PagM_AAM37_NC_048766(2),PHAGE_Salmon_BP63_NC_031250(2),PHAGE_Xantho_vB_XveM_DIBBI_NC_017981(2),PHAGE_Salmon_SPN3UB_NC_019545(2),PHAGE_Salmon_SJ46_NC_031129(2),PHAGE_Rhizob_RHEph06_NC_027296(2),PHAGE_Pantoe_vB_PagM_PSKM_NC_048767(2),PHAGE_Rhizob_RHEph04_NC_041908(2),PHAGE_Escher_Lys12581Vzw_NC_049917(2),PHAGE_Escher_HK639_NC_016158(2),PHAGE_Salmon_ZCSE2_NC_048179(2),PHAGE_Endosy_APSE_1_NC_000935(1),PHAGE_Salmon_UPF_BP2_NC_048649(1),PHAGE_Escher_Mangalitsa_NC_048799(1),PHAGE_Proteu_Myduc_NC_048803(1),PHAGE_Erwini_vB_EhrS_59_NC_048198(1),PHAGE_Proteu_VB_PmiS_Isfahan_NC_041925(1),PHAGE_Escher_ST31_NC_047829(1),PHAGE_Salmon_epsilon15_NC_004775(1),PHAGE_Bdello_phi1422_NC_019525(1),PHAGE_Pseudo_phi3_NC_030940(1),PHAGE_Klebsi_vB_KpnM_KpV79_NC_042041(1),PHAGE_Escher_vB_EcoM_Alf5_NC_031082(1),PHAGE_Stx2_c_Stx2a_F451_NC_049924(1),PHAGE_Bacter_APSE_2_NC_011551(1),PHAGE_Edward_MSW_3_NC_020082(1),PHAGE_Salmon_SW9_NC_049459(1),PHAGE_Aeromo_vB_AsaM_56_NC_019527(1),PHAGE_Erwini_vB_EhrS_49_NC_048197(1),PHAGE_Escher_phi191_NC_028660(1),PHAGE_Escher_1_NC_041979(1),PHAGE_Salmon_SPN9CC_NC_017985(1),PHAGE_Escher_P13374_NC_018846(1),PHAGE_Burkho_BcepB1A_NC_005886(1),PHAGE_Salmon_UPF_BP1_NC_047875(1),PHAGE_Salmon_vB_SenS_Sasha_NC_047786(1),PHAGE_Shigel_Sf13_NC_042017(1),PHAGE_Salmon_SE4_NC_048764(1),PHAGE_Xantho_XcP1_NC_048147(1),PHAGE_Escher_PA2_NC_028449(1),PHAGE_Entero_PsP3_NC_005340(1),PHAGE_Klebsi_vB_KpnM_KpV52_NC_041900(1),PHAGE_Shigel_Sf17_NC_042076(1),PHAGE_Vibrio_vB_VchM_138_NC_019518(1),PHAGE_Xantho_Carpasina_NC_047962(1),PHAGE_Pectob_ZF40_NC_019522(1),PHAGE_Edward_PEi21_NC_021342(1),PHAGE_Pseudo_PS_1_NC_029066(1),PHAGE_Ralsto_RSA1_NC_009382(1),PHAGE_Iodoba_phiPLPE_NC_011142(1),PHAGE_Phage_Gifsy_1_NC_010392(1),PHAGE_Salmon_HK620_NC_002730(1),PHAGE_Escher_vB_EcoM_4HA13_NC_049466(1),PHAGE_Salmon_9NA_NC_025443(1),PHAGE_Entero_VT2phi_272_NC_028656(1),PHAGE_Entero_phi80_NC_021190(1),PHAGE_Salmon_118970_sal4_NC_030919(1),PHAGE_Serrat_MTx_NC_048759(1),PHAGE_Klebsi_JD001_NC_020204(1)   21                               74.28%                           50.20%                        
                                  3              3.9Kb                    incomplete(60)                integrase,tail,recombinase                   contig,24,at,1844608:1-3917          0                        9                       6                                2                                88.8%                            1                                no                               5                                PHAGE_Salmon_SJ46_NC_031129(2),PHAGE_Salmon_Fels_2_NC_010463(2),PHAGE_Salmon_RE_2010_NC_019488(2),PHAGE_Salmon_SP_004_NC_021774(1),PHAGE_Entero_mEp235_NC_019708(1),PHAGE_Entero_lambda_NC_001416(1),PHAGE_Entero_HK022_NC_002166(1),PHAGE_Phage_Gifsy_1_NC_010392(1),PHAGE_Salmon_SEN4_NC_029015(1),PHAGE_Salmon_SW9_NC_049459(1),PHAGE_Entero_HK106_NC_019768(1),PHAGE_Entero_HK97_NC_002167(1),PHAGE_Escher_500465_1_NC_049342(1),PHAGE_Salmon_ST64B_NC_004313(1),PHAGE_Entero_P1_NC_005856(1),PHAGE_Salmon_SEN8_NC_047753(1),PHAGE_Salmon_SEN1_NC_029003(1),PHAGE_Salmon_SEN5_NC_028701(1),PHAGE_Salmon_vB_SosS_Oslo_NC_018279(1),PHAGE_Entero_PsP3_NC_005340(1),PHAGE_Escher_pro483_NC_028943(1)   2                                22.22%                           44.98%                        
                                  4              21.2Kb                   intact(150)                   tail,protease,portal,terminase               contig,32,at,2678231:1-21223          0                        24                      24                               0                                100%                             0                                no                               3                                PHAGE_Phage_Gifsy_2_NC_010393(23),PHAGE_Salmon_Fels_1_NC_010391(17),PHAGE_Entero_mEp460_NC_019716(13),PHAGE_Entero_cdtI_NC_009514(12),PHAGE_Entero_c_1_NC_019706(8),PHAGE_Phage_Gifsy_1_NC_010392(8),PHAGE_Entero_mEp213_NC_019720(5),PHAGE_Entero_lambda_NC_001416(4),PHAGE_Entero_HK630_NC_019723(3),PHAGE_Entero_DE3_NC_042057(3),PHAGE_Entero_HK629_NC_019711(2),PHAGE_Entero_YYZ_2008_NC_011356(2),PHAGE_Entero_HK225_NC_019717(2),PHAGE_Entero_vB_EcoM_VR25_NC_028925(1),PHAGE_Entero_BP_4795_NC_004813(1),PHAGE_Entero_phi80_NC_021190(1),PHAGE_Entero_ES18_NC_006949(1),PHAGE_Escher_APCEc01_NC_029091(1),PHAGE_Stx2_c_Stx2a_F451_NC_049924(1),PHAGE_Salmon_SJ46_NC_031129(1),PHAGE_Entero_mEp237_NC_019704(1)   22                               95.83%                           53.78%                        
                                  5              20.3Kb                   intact(150)                   tail,plate,flippase,lysin                    contig,54,at,4216600:17767-38109          0                        27                      24                               2                                96.2%                            1                                no                               13                               PHAGE_Burkho_BcepMu_NC_005882(16),PHAGE_Burkho_phiE255_NC_009237(16),PHAGE_Rhizob_RR1_B_NC_021557(7),PHAGE_Vibrio_X29_NC_024369(4),PHAGE_Pseudo_JBD67_NC_042135(3),PHAGE_Pseudo_PPpW_3_NC_023006(3),PHAGE_Pseudo_JBD25_NC_027992(3),PHAGE_Pseudo_B3_NC_006548(2),PHAGE_Entero_SfI_NC_027339(2),PHAGE_Bacter_Lily_NC_028841(2),PHAGE_Pseudo_JBD18_NC_027986(2),PHAGE_Faecal_FP_Epona_NC_047910(2),PHAGE_Escher_520873_NC_049344(2),PHAGE_Shigel_SfIV_NC_022749(2),PHAGE_Escher_503458_NC_049341(2),PHAGE_Entero_SfV_NC_003444(2),PHAGE_Entero_Arya_NC_031048(1),PHAGE_Salmon_epsilon34_NC_011976(1),PHAGE_Entero_Mu_NC_000929(1),PHAGE_Salmon_SJ46_NC_031129(1),PHAGE_Ralsto_RP12_NC_041911(1),PHAGE_Ralsto_RSA1_NC_009382(1),PHAGE_Escher_D108_NC_013594(1),PHAGE_Prochl_P_SSM7_NC_015290(1),PHAGE_Burkho_KS10_NC_011216(1),PHAGE_Entero_fiAA91_ss_NC_022750(1),PHAGE_Entero_P88_NC_026014(1),PHAGE_Haemop_SuMu_NC_019455(1),PHAGE_Pseudo_vB_PaeS_PM105_NC_028667(1),PHAGE_Shigel_SfII_NC_021857(1),PHAGE_Escher_RCS47_NC_042128(1),PHAGE_Cronob_ENT47670_NC_019927(1),PHAGE_Ralsto_RSY1_NC_025115(1),PHAGE_Haemop_Aaphi23_NC_004827(1),PHAGE_Salmon_SW9_NC_049459(1),PHAGE_Entero_UAB_Phi20_NC_031019(1),PHAGE_Salmon_SP_004_NC_021774(1),PHAGE_Escher_vB_EcoM_ep3_NC_025430(1),PHAGE_Entero_P1_NC_005856(1),PHAGE_Ralsto_RsoM1USA_NC_049432(1),PHAGE_Stenot_Smp131_NC_023588(1),PHAGE_Salmon_SPN9CC_NC_017985(1),PHAGE_Burkho_ST79_NC_021343(1)   7                                59.25%                           50.29%                        
