gi|323169733|ref|ADUU00000000.1| Shigella sonnei 53G gss53G.assembly.100, whole genome shotgun .5185984, GC%: 50.74%, length = 5185984 bps

Total : 30 prophage regions have been identified, of which 18 regions are intact, 6 regions are incomplete, 6 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 30.9Kb intact 150 42 1-30942 Prophage Escherichia coli CFT073 48.58% Detail
2 63.3Kb intact 150 72 163474-226849 Enterobacteria phage Mu 52.30% Detail
3 40.9Kb intact 150 39 233910-274900 Prophage Escherichia coli str. K-12 substr. MG1655 52.12% Detail
4 42.1Kb intact 150 57 369751-411895 PHAGE_Yersin_413C 52.06% Detail
5 46.5Kb intact 150 50 635956-682536 Enterobacteria phage HK629 51.27% Detail
6 27.3Kb incomplete 40 11 781697-809031 Salmonella phage SSU5 51.98% Detail
7 14.5Kb questionable 90 18 928933-943432 Enterobacteria phage phiP27 49.69% Detail
8 45.5Kb intact 150 65 1189146-1234679 Enterobacteria phage HK630 50.82% Detail
9 20.5Kb intact 120 26 1325714-1346225 Prophage Escherichia coli CFT073 49.51% Detail
10 26.9Kb intact 150 32 1699571-1726497 Enterobacteria phage phiP27 51.76% Detail
11 27.2Kb intact 140 23 1780999-1808254 Prophage Escherichia coli CFT073 48.79% Detail
12 47.8Kb intact 127 48 1971678-2019521 PHAGE_Yersin_413C 51.68% Detail
13 24.3Kb intact 97 32 1992668-2017048 PHAGE_Yersin_413C 54.17% Detail
14 21.3Kb intact 140 18 2160508-2181868 Prophage Escherichia coli CFT073 50.30% Detail
15 11.5Kb incomplete 50 16 2282612-2294132 Prophage Escherichia coli CFT073 50.75% Detail
16 24.7Kb questionable 90 21 2305543-2330328 Prophage Escherichia coli str. K-12 substr. MG1655 50.34% Detail
17 26.3Kb intact 150 25 2313865-2340210 Enterobacteria phage P1 52.37% Detail
18 23.9Kb intact 130 41 2524136-2548128 Salmonella phage ST64B 50.99% Detail
19 15.3Kb questionable 90 23 2550135-2565527 Prophage Escherichia coli str. K-12 substr. MG1655 51.20% Detail
20 28.4Kb intact 150 32 2712737-2741191 Prophage Escherichia coli CFT073 49.12% Detail
21 19.8Kb questionable 70 2811705-2831562 Synechococcus phage S-CBS1 41.57% Detail
22 22.7Kb intact 140 15 2814640-2837401 PHAGE_Entero_4795 42.42% Detail
23 15.3Kb intact 150 23 2933273-2948630 Prophage Escherichia coli CFT073 50.70% Detail
24 5.2Kb incomplete 50 3010926-3016140 Cronobacter phage ENT39118 45.04% Detail
25 19Kb incomplete 50 11 3406355-3425395 Enterobacteria phage phiP27 51.24% Detail
26 27.4Kb incomplete 40 11 3821466-3848882 Enterobacteria phage P1 47.70% Detail
27 30.7Kb questionable 80 20 3831270-3861998 Cronobacter phage ENT39118 48.99% Detail
28 31.7Kb intact 130 24 3918088-3949815 Prophage Escherichia coli CFT073 48.14% Detail
29 16.6Kb incomplete 60 23 4715747-4732427 Enterobacteria phage P1 49.16% Detail
30 13.8Kb questionable 80 20 5171890-5185783 Prophage Escherichia coli CFT073 49.09% 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.