SAMtools - Pileup format question

[cliff]

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.

[nilshomer]

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.

Check your FASTA reference file. The upper and lower bases indicate repeat mask sequence (can't remember which, see UCSC).

[Thomas Doktor]

Lowercase indicate repeat sequences. This is known as soft masking. Hard masking will print N instead of the lowercase bases.

[lh3]

It is determined by your reference sequence.