Dear All
I just noticed that in my pileup file there are rows like these:
chr10 59083 c T 40 123 26 41 TTTTtTTT,,T.,Tttt,.,tTttttttTttttTtt,TT,^FT ECF#H9H=H@#EB@HC?5HFAHHB@GEH@FE>=;?ADHECB
chr10 61647 G R 58 58 35 19 .AAAA,,,A,A.A,A.A.a 0<G':HDHBGAEH36FBF#
chr10 61776 t C 37 78 32 20 CCc$.$CCCcccCcccCCC,,c 8#A#2#?CBBBF>9H@=###
I know from SAM FAQ http://sourceforge.net/apps/mediawik...?title=SAM_FAQ
that the third column is "reference base". But, what is the difference between the uppercase (G) and lowercase (c and t) letters here?
Any answer will be appreciated.
I just noticed that in my pileup file there are rows like these:
chr10 59083 c T 40 123 26 41 TTTTtTTT,,T.,Tttt,.,tTttttttTttttTtt,TT,^FT ECF#H9H=H@#EB@HC?5HFAHHB@GEH@FE>=;?ADHECB
chr10 61647 G R 58 58 35 19 .AAAA,,,A,A.A,A.A.a 0<G':HDHBGAEH36FBF#
chr10 61776 t C 37 78 32 20 CCc$.$CCCcccCcccCCC,,c 8#A#2#?CBBBF>9H@=###
I know from SAM FAQ http://sourceforge.net/apps/mediawik...?title=SAM_FAQ
that the third column is "reference base". But, what is the difference between the uppercase (G) and lowercase (c and t) letters here?
Any answer will be appreciated.
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