gi|327178510|ref|AEZJ00000000| Escherichia coli 97.0246 whole genome shotgun .5475907, GC%: 50.60%, length = 5475907 bps

Total : 25 prophage regions have been identified, of which 15 regions are intact, 5 regions are incomplete, 5 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 57.9Kb intact 150 63 306-58254 Enterobacteria phage HK630 50.57% Detail
2 41.8Kb intact 150 65 131855-173689 PHAGE_Entero_4795 49.44% Detail
3 29.3Kb questionable 80 50 386203-415511 Escherichia phage TL-2011c 49.41% Detail
4 13.7Kb questionable 75 16 691559-705320 Enterobacteria phage P4 52.76% Detail
5 17Kb intact 107 27 1354053-1371110 Enterobacteria phage P4 45.81% Detail
6 42.5Kb incomplete 30 28 1757401-1799988 Enterobacteria phage mEp460 49.97% Detail
7 45Kb intact 150 61 1867886-1912894 Enterobacteria phage P4 51.64% Detail
8 15.3Kb intact 100 19 2028709-2044050 PHAGE_Entero_2008 55.04% Detail
9 86Kb intact 150 104 2138076-2224158 PHAGE_Entero_4795 48.43% Detail
10 54.9Kb intact 150 75 2316357-2371306 PHAGE_Entero_4795 48.36% Detail
11 24.5Kb intact 100 24 2382466-2407040 Enterobacteria phage HK630 44.34% Detail
12 6.3Kb incomplete 30 2894478-2900806 PHAGE_Stx2_c_II 54.46% Detail
13 43.6Kb intact 100 28 2966167-3009817 Enterobacteria phage P4 49.62% Detail
14 45.7Kb intact 150 55 3014336-3060045 Enterobacteria phage HK630 51.89% Detail
15 49.3Kb intact 150 64 3623156-3672497 Enterobacteria phage phiP27 51.81% Detail
16 36.9Kb intact 150 56 3710069-3747009 PHAGE_Yersin_413C 52.25% Detail
17 6.6Kb questionable 70 3774989-3781641 Stx2-converting phage 1717 54.08% Detail
18 16.5Kb questionable 90 30 3807414-3823951 PHAGE_Entero_4795 51.34% Detail
19 8.4Kb incomplete 50 10 4558452-4566853 Enterobacteria phage cdtI 49.39% Detail
20 35.2Kb intact 123 47 4717557-4752782 PHAGE_Yersin_413C 51.73% Detail
21 23.2Kb questionable 90 31 4729519-4752782 PHAGE_Yersin_413C 54.92% Detail
22 47.1Kb intact 150 65 4842424-4889567 PHAGE_Entero_4795 52.51% Detail
23 10.6Kb incomplete 40 15 5182477-5193104 Cellulophaga phage phiST 51.67% Detail
24 56Kb intact 150 75 5199004-5255085 Enterobacteria phage HK630 50.26% Detail
25 9.6Kb incomplete 60 19 5325544-5335226 PHAGE_Entero_2008 45.21% Detail
Legend:
REGION: the number assigned to the region
REGION_LENGTH: the length of the sequence of that region (in bp)
COMPLETENESS: a prediction of whether the region contains a intact or incomplete prophage based on the above criteria
SCORE: the score of the region based on the above criteria
#CDS: the number of coding sequnce
REGION_POSITION: the start and end positions of the region on the bacterial chromosome
PHAGE: the phage with the highest number of proteins most similar to those in the region
GC_PERCENTAGE: the percentage of gc nucleotides of the region
DETAIL: detail info of the region


txt file for download


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.