Fig. 1

Mismatch rates detected from mapping reads to reference genome. Reads from Group A (all reads) were mapped to reference genomes as paired-end reads or single end reads (R1 and R2 shuffled together). Reads from Group M (reads can be merged together) were mapped as paired-end reads or merged single reads. Mismatch rates for Group A and Group M are explored. For raw reads (a), the mismatch rates of Group A were similar for both paired-end mapping and shuffled reads mapping. The rate decreased significantly for Group M (paired-end) and decreased even more for Group M (merged reads). For trimmed reads (b), there was much less decrease or even increase of mismatch for large libraries (500 bp and 600 bp). The difference of mismatch rates between Group M (paired reads) and Group M (merged reads) was tested by paired t tests