SNPs in CHM were detected from two methods. (1) We compared the CHM genome to the HN1 genomes using the lastz-chainnet pipeline12. CHM and HN1 genome alignment was performed using lastz (version 1.02.00) (, and alignment statistics were generated with an in-house Perl script. Then, SNP sites were identified using an in-house Perl script. (2) We detected heterozygous SNPs using GATK based on alignments of short reads of HN1 onto assembled CHM genomes. Then, we located these heterozygous SNP sites on the CHM genome according to the one-to-one genome alignment results.

SV detection was carried out using lumpy (version 0.2.13, First, short reads of CHM were mapped to HN1 genomes using BWA (version 0.7.8)48. After BWA alignment, the bam file was sorted and indexed using SAMtools (version 1.10)49. We then detected SV using lumpy (version 0.2.13) with default parameters.