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 04-27-2010, 08:23 AM #1 mr_boourns Junior Member   Location: New Haven Join Date: Apr 2010 Posts: 2 maq mapcheck Hi all, I was wondering does anyone have any experience using maq mapcheck to estimate the different substitution rates by substitution type. After an RNAseq analysis I get the following as the first 3 lines of the mapcheck file. 1 20.4 23.2 29.0 27.5 : 7 18 8 6 7 11 3 3 2 4 7 5 : 5 10 14 969 : 72 41 29 18 2 23.2 25.1 30.7 21.1 : 4 11 3 4 5 5 2 2 1 3 6 4 : 6 11 14 969 : 115 40 24 11 3 28.1 23.8 33.0 15.0 : 2 7 1 2 2 3 2 1 0 2 5 3 : 5 10 14 969 : 29 20 14 6 As far as I understand I can approximate the overall substitution rate for cycle 1 from the last 8 columns of the first row. as (969/1000)*(18/1000)+(14/1000)*(29/1000)+(41/1000)*(10/1000)+(72/1000)*(5/1000) = 0.018. The columns in the middle represent the substitution rates by substitution type. i.e. For all A's in the reference genome, 7/1000 of the alligned reads had a C in this position. Is this the correct interpretation? Sorry if this question seems quite simple. Thanks, John