#### Version 1 This version of the analysis was used in the Toh et al. 2022 Nile rat genome paper. This analysis is to detect the full spectrum of heterozygosity in Nile rat's haplotype assemblies, which is only focused on the autosomes, **not including the sex chromosomes and unanchored scaffolds.** Thus, the FASTA file maternal/mat.chrs.fa.gz only contains the curated scaffolds of chromosomes 1-31 (hypothetical by length). If you want to get a real complete haplotype assembly, you need to include the remaining parts. The remaining parts can be retrieved by its scaffold id (like mat.original.remain.scaf.ids). The paternal follows the same rule. File descriptions: - alignment of these to the principal pseudohaplotype from RefSeq: Refseq_annot_liftover/pat_as_query_lastz/refseq_vs_pat.chain.gz, Refseq_annot_liftover/mat_as_query_lastz/refseq_vs_mat.chain.gz - lifted-over annotations: Refseq_annot_liftover/*.bed - coordinates of heterozygous features: Variants/variants/*.txt - the list of genes affected by various types of heterozygosity: Variants/*.bed #### Version 2 We discovered a misassembly in the paternal chr1, which we used to detect genetic diversity. Then we decided to update the analysis. We do not believe that this revision materially affects the results reported in the Toh et al. 2022 Nile rat genome paper. In previous analysis, the maternal and paternal haplotypes were improved by reciprocal validation; however, we did not use any information from Refseq version, which is a curated version of pat+X. When compared to pat+X, the sequence JAAOME010000023.1 in maternal incorrectly combined NW 023044999.1 and NW 023045000.1. In this new version, we chose all autosome chromosomes from the Refseq version as the standard, as well as the paternal haplotype. The maternal haplotype assembly was then mapped to this reference in order to improve maternal assembly by scaffolding small unanchored sequences. Then, split JAAOME010000023.1 at the correct location. This update simply fixes the misassembly, and we don't believe there is a significant difference in results, unless some SVs are located at these breakpoints. Files *pat.id* and *matChrs_from_ncbi.agp* provide mappings between paternal and maternal chromosomes used in this analysis and NCBI scaffold accessions.