gi|323186640|ref|ADUR00000000.1| Escherichia coli 1357 OK1357.assembly.100, whole genome shotgun .5277070, GC%: 50.61%, length = 5277070 bps

Total : 18 prophage regions have been identified, of which 13 regions are intact, 1 regions are incomplete, 4 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 5.4Kb questionable 80 1248-6742 PHAGE_Gifsy_1 55.27% Detail
2 109.8Kb intact 130 127 25606-135414 Enterobacteria phage P1 48.10% Detail
3 41.2Kb intact 150 51 375172-416383 PHAGE_Yersin_413C 51.58% Detail
4 52.5Kb intact 150 47 571010-623572 Enterobacteria phage HK629 49.90% Detail
5 46.9Kb intact 150 61 1024089-1071017 PHAGE_Gifsy_1 50.35% Detail
6 22Kb intact 150 32 1364932-1386972 Enterobacteria phage 285P 53.97% Detail
7 33.5Kb intact 150 46 1364932-1398474 Enterobacteria phage 285P 50.58% Detail
8 32.8Kb intact 96 21 1983638-2016534 Enterobacteria phage P4 50.12% Detail
9 10.7Kb questionable 90 11 2526415-2537166 Stx2-converting phage 1717 47.67% Detail
10 5.9Kb questionable 80 10 2687424-2693377 Enterobacteria phage cdtI 49.73% Detail
11 22.2Kb intact 101 30 2826389-2848621 PHAGE_Yersin_413C 54.48% Detail
12 42.3Kb intact 135 46 2819480-2861827 PHAGE_Yersin_413C 51.17% Detail
13 8.5Kb intact 107 12 2913175-2921768 Enterobacteria phage P4 53.36% Detail
14 11.7Kb intact 117 15 4682870-4694594 Enterobacteria phage P4 49.39% Detail
15 19.1Kb intact 107 17 5142849-5161975 Enterobacteria phage P4 50.58% Detail
16 13.8Kb questionable 90 24 5162991-5176838 Enterobacteria phage SfV 49.29% Detail
17 18.6Kb incomplete 60 36 5219857-5238488 Salmonella phage 19 47.41% Detail
18 33Kb intact 150 25 5234106-5267170 Enterobacteria phage HK629 47.46% 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.