Of the experiments, two pairs of replicates (305_nasal and 305_cell_cond1) were amplified under the same optimal experimental conditions while each of the other pairs (305_cell_cond2, 305_cell_cond3, 305_cell_cond4, 305_cell_cond5) were amplified under different suboptimal experimental conditions (simulating experimental volatility). Compared with the available capillary sequences for sample 305, EvolSTAR had an average error rate of 0.0012% and 28 ambiguous calls per sample (338 in total). On the other hand, Nimblescan A  CGT  547  246  CTG  558  237  GCT  957  367  GTC  2215  1407  TCG  1049  611  TGC  3015  2873   C  AGT  2035  2712  ATG  1752  2400  GAT  382  341  GTA  159  134  TAG  360  377  TGA  165  129   G  ACT  1474  1043  ATC  976  624  CAT  1639  1534  CTA  868  788  TAC  594  410  TCA  542  454   T  ACG  432  529  AGC  562  636  CAG  623  841  CGA  1066  1616  GAC  1421  1878  GCA  1637  2841 Hybridization intensity reduction orders found in 25 028 true calls from two replicated hybridization experiments of patient sample 380. For each true call, for each strand, we rank the PM probe and its MM probes based on their hybridization intensities in decreasing order. We count the frequency of each hybridization intensity reduction order. 1  6002  6  5888  6  0  0  EvolSTAR  2  6002  6  5993  6  0  0  PBC  2  6002  6  5895  6  0  1   507  EvolSTAR  1  3921  8  3913  8  0  0  PBC  1  3921  8  3736  8  0  3  EvolSTAR  2  3921  8  3916  8  0  0  PBC  2  3921  8  3758  8  0  2   581  EvolSTAR  1  8574  10  8567  10  0  0  PBC  1  8574  10  8458  10  0  2  EvolSTAR  2  8574  10  8566  10  0  0  PBC  2  8574  10  8461  10  0  5   582  EvolSTAR  1  3057  4  3051  4  0  0  PBC  1  3057  4  2986  4  0  0  EvolSTAR  2  3057  4  3053  4  0  0  PBC  2  3057  4  3001  4  0  0  593  EvolSTAR  1  3054  3  3053  3  0  0  PBC  1  3054  3  3007  2  1  0  EvolSTAR  2  3054  3  3053  3  0  0  PBC  2  3054  3  2992  2  1  0   9 061 364  EvolSTAR  1  5129  5  5123  5  0  0  PBC  1  5129  5  5064  5  0  0  EvolSTAR  2  5129  5  5122  5  0  0  PBC  2  5129  5  5042  5  0  0   9 061 365  EvolSTAR  1  3000  3  2993  3  0  0  PBC  1  3000  3  2956  3  0  1  EvolSTAR  2  3000  3  2991  3  0  0  PBC  2  3000  3  2941  3  0  0   9 061 366  EvolSTAR  1  1683  3  1683  3  0  0  PBC  1  1683  3  1649  3  0  1  EvolSTAR  2  1683  3  1682  3  0  1  PBC  2  1683  3  1636  3  0  1   923  EvolSTAR  1  4373  5  4365  5  0  0  PBC  1  4373  5  4187  5  0  1  EvolSTAR  2  4373  5  4330  5  0  1  PBC  2  4373  5  3738  5  0  6 Types of calls and their frequencies generated by EvolSTAR and PBC in replicated microarray hybridizations of 14 patient samples. Partial or complete capillary sequences were generated for each sample and used to verify the calls made by EvolSTAR and PBC on each replicate. We then count the frequency of true-non-mutation, true-mutation, error and 'N' calls in each replicate.