gi|345049058|ref|ACWM00000000.1| Desulfovibrio sp. 6_1_46AFAA .1, whole genome shotgun .3826115, GC%: 61.06%, length = 3826115 bps

Total : 10 prophage regions have been identified, of which 4 regions are intact, 5 regions are incomplete, 1 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 97.2Kb intact 120 94 167594-264885 Escherichia phage phAPEC8 58.41% Detail
2 35.4Kb intact 150 51 1041448-1076847 Haemophilus phage SuMu 61.20% Detail
3 31.1Kb questionable 80 27 1151309-1182476 Salmonella phage SPN1S 60.88% Detail
4 21.7Kb incomplete 50 31 1804894-1826611 Burkholderia phage BcepMu 64.48% Detail
5 38.1Kb intact 130 47 2662520-2700622 Haemophilus phage Aaphi23 63.01% Detail
6 44.2Kb intact 100 35 3068729-3112963 Salmonella phage SPN1S 58.54% Detail
7 8.8Kb incomplete 30 3206842-3215713 PHAGE_Anguil_1 57.96% Detail
8 59.1Kb incomplete 60 49 3348393-3407536 Burkholderia phage DC1 60.65% Detail
9 21.4Kb incomplete 50 25 3759306-3780773 Pelagibacter phage HTVC011P 62.74% Detail
10 9.1Kb incomplete 60 13 3815931-3825039 Prophage Brucella suis 1330 56.18% 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.