I have a bacteria on lab and have its reference genome so what would be the best coverage for "total length (Mb): 4.21561" of a bacterial genome sequenceing? and hiseq or miseq?
That depends on desired or possible read length, downstream application (why sequence it) and repetitive content of the genome.
Try Illumina's sequencing coverage calculator.
Since you have a reference available coverage you want would depend on what you are trying to do as @decosterwouter said above.
If you are looking to call SNP's (or do rearrangement analysis) then 5-10x coverage may be enough. If your strain turns out to differ significantly from the reference (and many strains might depending on how long they have been cultured/in use in your lab) you may need to assemble a new reference for your strain.
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version 2.3.6
I would like to do whole genome sequencing (4,000,000bp) of a bacteria which has a reference sequence. so I won't do de novo assembly I will do reference based assembly. So what is your opinion?
MiSeq should be sufficient to cover a genome like that, MiSeq V3 has ~45M 300bp paired-end reads (depending on cluster density). Just rough calculation: 40 million reads of 300bp => 3000 fold coverage which is an enormous/outrageous over sequencing. You definitely don't need HiSeq for this, but offcourse it depends on what machines you have available and/or the prices of your sequencing provider.
Since your genome is haploid about 5-15 fold coverage should be fine for calling SNPs...