Additional file 4 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

Additional file 4 This table contains multiple tabs. Tab 1 reports results from the comparison of the mLinker haplotype solution of the RPE-1 genome generated from 60 × linked-reads and Hi-C sequencing data to the reference haplotype data derived from sequencing of monosomic chromosomes. Tabs 2-5 report results from the comparison of the mLinker haplotype resolution generated from downsampled linked-reads and Hi-C data. Tab 6 reports benchmark metrics of the mLinker haplotype solution generated from 11 × PacBio HiFi data and Hi-C data. In Tab 1, the comparison is performed on both the scaffold haplotype solution and the final haplotype solution filtered by haplotype linkage. In Tabs 2-5, the comparison is only performed on the scaffold haplotype solution. For each mLinker solution in Tabs 1-5, we report results from the comparison of phased genotypes at all phased variant sites (“No filter”), at phased sites not in centromeric/acrocentric regions (“Excluding centromere”), and at phased sites also passing the allele fraction filter from single-cell data (“allele filter from single-cell data”). In Tab 6, we report results from two separate calculations, the first using all variants as input, the second using only high-quality variants (sites that pass the linkage filter in the mLinker final haplotype solution derived from linked-reads and Hi-C data). The comparison in Tab 6 is only performed on high-quality variants.附加文件4 本表包含多个分表。分表1展示了基于60×连锁读段（linked-reads）与Hi-C测序数据生成的RPE-1基因组mLinker单倍型（haplotype）解，与源自单体染色体测序的参考单倍型数据的比对结果。分表2至5展示了基于降采样连锁读段与Hi-C数据生成的mLinker单倍型解析结果的比对情况。分表6展示了基于11×PacBio HiFi测序与Hi-C数据生成的mLinker单倍型解的基准评测指标。在分表1中，比对同时针对支架单倍型解，以及经单倍型连锁过滤后的最终单倍型解开展。在分表2至5中，比对仅针对支架单倍型解进行。针对分表1至5中的每一组mLinker解，我们报告了三类比对结果：所有分型变异位点的分型基因型比对（"无过滤"）、非着丝粒/近端着丝粒区域的分型变异位点的分型基因型比对（"排除着丝粒区域"），以及通过单细胞数据等位基因比例过滤的分型变异位点的分型基因型比对（"单细胞数据等位基因过滤"）。分表6中，我们报告了两组独立计算的结果：第一组以全部变异位点作为输入，第二组仅使用高质量变异位点，即源自连锁读段与Hi-C数据的mLinker最终单倍型解中通过连锁过滤的位点。分表6中的比对仅针对高质量变异位点开展。