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Fig. S1 Frequency distribution of mean quality score of individual CCS reads before (untrimmed) and after quality control (trimmed).

Fig. S2 Homopolymer lengths of CCS reads.

Fig. S3 The number of CCS reads generated by a single SMRT cell.

Fig. S4 Negative correlation between sequence quality and sequence length in raw CCS reads.

Fig. S5 Positive correlation between sequence quality and sequence length in post-QC CCS reads.

Fig. S6 Positive correlation between homopolymer length and raw CCS read length.

Fig. S7 Base position GC content of CCS reads before (black) and after quality control (grey).

Table S1 Simulations of microsatellite detection effectiveness in relation to read length when sequencing errors were not introduced.

Table S2 Simulations of microsatellite detection effectiveness in relation to read length when PacBio CCS error profiles (Ono et al. 2013) were used.

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