demystify pileup format -- how to properly filter pileup format

Question

[Lhl]

Hi Folks,

I just found that with perl regex, I got variants frequencies that summed up to exceed sequencing depth.

cut -f5 test.pileup | perl -ne 'chomp; @del = $_ =~ /-\d+[AGCTN]/ig; @ins= $_ =~ /+\d+[AGCTN]/ig; @m = $_ =~ /./g; print scalar (@del) ."\t". scalar (@ins). "\t". scalar (@m). "\n";' 128 23 3781

obviously the number of deletions + number of insertions + number of (mis)matches > coverage

Can anyone explain why? Did I make mistake?

Thanks a lot.

The test.pileup file content is shown below:

contig1      200      T       3789    ...-1G....-1G.........+1G...........................-1G........-1G...........................-1G..............-1G.-1G.....-1G....*....-1G................-1G............C..C.............-1G*...........-1G..................................-1G..................................-1G............-1G..-1G...................-1G.......*......-1G...................................*.........................................*.......-1G.-1G.....-1G..............................-1G........................+1G.-1G.-1G....................................-1G......-1G..-1G.......+1G...........-1G.+1G......-1G....................+1G.........................-1G...........-1G..........-1G....................-1G........................-1G...........................................-1G..............-1G...-1G............................-1G.......-1G........-1G......................................................-1G.............-1G...-1G.-1G..................-1G......-1G.-1G...................+1G.................................-1G...-1G...................................................-1G......................+1G.................-1G...................-1G.................-1G.............-1G.........-1G............-1G........-1G....................................-1G..............-1G..-1G..-1G......+1G.............-1G......-1G..........................-1G..-1G......-1G.....-1G.......-1G................-1G....-1G..-1G................-1G.........................+1G....................................+1G...................+1G................-1G........-1G....................................-1G.-1G.....-1G......-1G.....-1G........-1G............................C..............-1G.......-1G......-1G..........-1G...-1G..............+1G....+1G...........................-1G.......-1G......-1G..........+1G.-1G.............-1G.-1G........-1G....-1G......................-1G.....-1G.....-1G.-1G..-1G.-1G...........-1G................-1G.....+1G...............-1G...............+1G....-1G.......-1G....................+1G........-1G...........-1G..+1G..............................+1G...........................-1G.................-1G..-1G.........+1G...............-1G...-1G.........-1G........................................-1G....-1G..............................................-1G...+1G...........................-1G...-1G..........-1G..+1G.-1G.-1G...-1G...................................................-1G............-1G.....-1G........................-1G........................................+1G............................-1G.-1G......-1G...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................^].^].^".^].^].^].^3.^].^'.^2.^].^].^].^].^].^].^].^].^].^D.^].^].^7.^".^].^].^;.^].^5.^N.^].^].^].^].^].^].^].^C.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^V.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^6.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^A.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^=.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^R.^].^].^].^].^C.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^>.^N.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^Y.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^H.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^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