Mycobacteriophage J1
The whole genome sequencing of the J1 Mycobacteriophage was performed on IIlumina Next Generation Sequence (NGS) 500 platform with 2150 bp chemistry. The DNA was extracted from PEG precipitated, J1 mycobacteriophage sample using cTab and Phenol:chloroform extraction method  followed by RNase treatment. The purity of the extracted DNA was determined using Nano Drop spectrophotometer. The DNA sample after clearing quality control was processed for library preparation. Quantification and sizing of DNA fragments were assessed on Agilent 4200 Tape Station using Agilent High Sensitivity D1000 Screen Tape assay. The Genomic DNA Screen Tape assay was used to monitor the efficiency of the focused ultrasonication in shearing gDNA and high sensitivity D1000 ScreenTape was used to determine size distribution of the fragments.The average size of gDNA library was found to be 533bp. The paired-end sequencing library prepared using Illumina Tru Seq Nano DNA library kit yielded a total of ~1.39 Gb data. The sequenced data obtained was processed to eliminate adapter sequences, ambiguous reads and low quality sequences and any host reads that may have been present. The high quality reads of the J1 Mycobacteriophage sample were mapped against the reference host bacterium Mycobacterium smegmatis genome, to eliminate any host reads that may be present and yielded a total of ~130Mbp data. The host filtered genome was assembled using SPAdes and the assembled genome was quality assessed using Quast. The assembled genome was annotated using Prokka. The Prokka analysis yielded 5432 contigs, totalling 6673045 bp. The annotated genome sequence containing 6673,045 bp obtained through Prokka was then uploaded on the webserver - PHAST (PHAge Search Tool). The prophage regions within the Prokka annotated genome were identified and annotated using PHAST. PHAST web server identified 9 regions containing prophage sequences within the annotated genome sequence. The annotated phage proteins or phages like proteins were then identified by performing a BLAST search against PHAST's local phage/prophage sequence database along with specific keywords searches to facilitate further refinement and identification. Matched phage or phage like sequences with BLAST e -values less than 10 4 were saved as hits and their positions tracked for subsequent evaluation. In addition to these basic operations, PHAST also evaluated the completeness of the putative prophage regions. Of the 9 regions obtained with the J1 genome sequence, 2 regions namely Region 4 and Region 6 have being identified as intact prophage regions. Cornerstone genes encoding proteins involved in phage structure, DNA regulation, insertion and lysis were found to be present in the J1 mycobacteriophage genome. The presence of key phage proteins such as integrase, portal protein, terminase, and tail tape measure protein were also noted. These proteins are known to serve as prophage markers for temperate phages. Besides the cornerstone structural component genes and the four marker proteins (integrase, portal protein, terminase, tail tape measure protein) found in J1 prophage regions, presence of other significant proteins were also seen; namely genes coding for proteins involved in host lysis such as Peptidoglycan hydrolase (an endolysin) and Holins.