Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays

Lee, Charlie Wah Heng; Koh, Chee Wee; Chan, Yang Sun; Aw, Pauline Poh Kim; Loh, Kuan Hon; Han, Bing Ling; Thien, Pei Ling; Nai, Geraldine Yi Wen; Hibberd, Martin L.; Wong, Christopher W.; Sung, Wing-Kin

For query bases that results in a mutation call but have NHIP of type described in Figure 2c , they are most likely isolated errors caused by poor PM probe quality. Hence, we correct the base-calls of these query bases to their respective reference bases (but represented by lower case Figure 2 . Summary of characteristics of neighbourhood hybridization intensity profiles for different type of calls. Summary of the characteristics of the NHIP for five types of call: (a) true-non-mutation, (b) true-mutation, (c) isolated error or 'N', (d) long chains of consecutive errors or 'N', (e) unknown error or 'N') based on their respective observed neighbourhood hybridization intensity profiles. The PM probe (red circle) of query base is at position 0 while neighbourhood PM probes (black circles) are numbered according to their distance away from the query base. A PM probe is significantly differentiated from its MM probes if its hybridization intensity is at least t-fold that of all its MM probes. base calls 'a', 'c', 'g' or 't') in the reference sequences. We also perform the same correction to non-high-confidence query bases with NHIP of type described in Figure 2c .