Fig. 6

Complete discordances covered by long reads. Two complete discordances were detected using CCS reads. Correspondingly, in ONT reads and Corrected reads, the discordance rates (coverage tracks) were close to 100% and 50%, respectively. It suggests that the genotypes of ONT raw reads were consistent with that of CCS reads, but the error-correction process introduces errors, resulting in nearly half of the genotypes of the corrected reads being different from CCS reads. Multiple reads are secondary mapping (blank strips) in the ONT reads alignments, and their primary alignments were in other homologous regions, which may interfere with the error-correction process. The blue, red, green, and orange blocks represent “C”, “T”, “A”, and “G” genotypes, respectively. Gray and blank strips represent primary alignment and secondary alignment, respectively