By El-Sayed Bahaa Machaly
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Extra resources for Behavior, Analysis and Design of Steel Work Connections
5b) and the error probabilities allow us to estimate how large the uncertainty for correct base calls becomes. 0001 49 40 30 20 10 0 0 5 10 15 20 25 30 35 40 ! " #$%&' ( ) * + , − . / 0123456789 : ; <= . @ABCDEFGH 1 5 10 15 20 25 30 35 Position in read Quality Score and one−letter ASCII code using offset 33 Fig. 5 (a) Quality scores: Conversion between error probabilities and Phred-type quality scores. The quality score Q is calculated from the error probability e by Q ¼ À10 Â log e and can be represented as an ASCII character, here using an offset 33.
3. There is a remarkable agreement between these points and the theoretical lines in the logarithmic plot. This is partially coincidental, and a close 48 Peter Menzel et al. 00 15 20 25 30 Read length Fig. 4 Fraction of reads from E. coli that have unique matches in the human genome. The fraction of all reads that map uniquely to the human genome is shown as a function of the read length. Individual curves are shown for matches with up to, respectively, 0, 1, 2, and 3 mismatches. The same reads and procedure as in Fig.
All these error sources result in a certain divergence between the read sequence and its genomic origin, which has to be accounted for by the mapping program. If a read maps to several locations in the genome, we ideally want to know which of these locations is the true origin. Thus, the mapper uses some criterion for this decision or, if it has multiple indistinguishable mappings, reports a read as multiple mapped. For example, the mappers BWA , MAQ , SOAP2 , and Bowtie2  report possible alternative matches.