The details of the RPM v.1 design and the experimental methods have been discussed in previous work (15, 16, 18) (Lin et al., submitted for publication). Briefly, the RPM v.1 chip design includes 57 tiled regions allowing resequencing of 29.7 kb of sequences from 27 respiratory pathogens and biothreat agents. These were selected based upon clinical relevance for the population of immediate interest (United States military recruit in training) (19) (20) (21) . Partial sequences from the genes containing diagnostic regions were tiled for the detection of these pathogens. The experimental microarray data used in the present analysis were obtained using a variety of purified nucleic acid templates and clinical samples culture (throat swabs and nasal washes) using random and multiplexed RT-PCR amplification schemes (for more detail description of amplification methods see Supplementary Data). Resequencing microarrays provide base call resolution by comparing the intensities between a set of four 25mer probes that differ from each other at the same position (13th base). An amplicon or target sequence is represented by numerous overlapping probe sets. GCOSÔ software v1.3 (Affymetrix Inc., Santa Clara, CA) was used to align and scan hybridized microarrays to determine the intensity of each probe in every probe set. Base calls were made based on the intensity data of each probe set using GDAS v3.0.2.8 software (Affymetrix Inc.) which used an implementation of the ABACUS algorithm (5) . The sequences were represented in FASTA format for later analysis steps.