Difference of coverage between amplicons
Well, to plot the coverage I would use something like Python Matplotlib. Take a look at this example:

import matplotlib.pyplot as plt
import matplotlib

amplicons =  ('TTGCCAGTTAACGTCTTCCTTCTCTCTCTG', 
      'CCCTTGTCTCTGTGTTCTTGTCCCCCCCA', 
      'TGATCTGTCCCTCACAGCAGGGTCTTCTCT', 
      'CACACTGACGTGCCTCTCCCTCCCTCCA')
countAmpl = (1635, 4734, 2156, 3085)

fig = plt.figure(figsize=(10,8.5))

subplt = fig.add_subplot(111)
subplt.set_ylabel('Count')
subplt.set_xlabel('Amplicons')
subplt.plot(amplicons, countAmpl,  linestyle='-', marker='o', color='blue')
for tl in subplt.get_yticklabels():
    tl.set_color('blue')

plt.savefig("amplicons.eps")


Check other types of charts in Matplotlib if you think you need something else.

You can also try to open and visualize the BAM in IGV from the Broad Institute.

Regarding the difference in coverage, I would say that some are from a repetitive region. Or the amplification depth of a region is greater than for the others. Or maybe the aligner found similar regions and decided that the amplicon aligns well in all those regions.