Additional file 2 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Creators: name: Jia, Peng
name: Dong, Lianhua
name: Yang, Xiaofei
name: Wang, Bo
name: Bush, Stephen J.
name: Wang, Tingjie
name: Lin, Jiadong
name: Wang, Songbo
name: Zhao, Xixi
name: Xu, Tun
name: Che, Yizhuo
name: Dang, Ningxin
name: Ren, Luyao
name: Zhang, Yujing
name: Wang, Xia
name: Liang, Fan
name: Wang, Yang
name: Ruan, Jue
name: Xia, Han
name: Zheng, Yuanting
name: Shi, Leming
name: Lv, Yi
name: Wang, Jing
name: Ye, Kai
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1. Length distribution of ONT reads in this study. Fig. S2. Haplotype-resolved assembly pipeline for the Chinese Quartet twins. Fig. S3. Alignments of paternal (top) and maternal (bottom) haplotypes to GRCh38. Fig. S4. Comparison between haplotype-resolved assemblies of the Chinese Quartet twin daughters and GRCh38 as well as CHM13. Fig. S5. Overview of the gaps in the assemblies of Chinese Quartet twin daughters. Fig. S6. Bar plots show the ratio of the number of abnormal bins to total the number of bins at both (a) chr17:21,523,754–22,371,820 (the regions covered in Fig. 1b) and (b) chr8: 6,281,267–13,968,020 (the region covered in Fig. 1c). Fig. S7. Dotplots between the Chinese Quartet twins assemblies and both the GRCh38 and CHM13-T2T (v2.0) at a region near the centromere of chromosome 17 (chr17:21,523,754-22,371,820). Fig. S8. Dotplots between the twins of the Chinese Quartet assemblies and both GRCh38 and T2T genomes at chromosome 8p23.1. Fig. S9. Circos plots show the characteristics of the paternal (A) and maternal (B) haplotypes of the Chinese Quartet twin daughters. Fig. S10. Distribution of novel sequence distribution in CQ-P (left) and CQ-M (right). Fig. S11. SNV and indel detection and validation pipelines. Fig. S12. Structural variant detection and validation pipelines. Fig. S13. Validated percentage of SNVs and indels across seven different combinations of three technologies. Fig. S14. Indel length distributions of HG002 and three technologies calls of Chinese Quartet twin daughters. Fig. S15. SNV rate in repeat regions across different combinations of three technologies. Fig. S16. Indel rate in repeat regions across different combinations of three technologies. Fig. S17. IGV show the alignment of HRAs, HiFi reads, and Illumina reads to the reference genome (GRCh38) in a 49bp homopolymer region. Fig. S18. Distribution analysis in homopolymer regions. Fig. S19. SV length distributions of HG002 and three callsets of Chinese Quartet twin daughters. Fig. S20. Large deletion rate in repeat regions across different combinations of three technologies. Fig. S21. Large insertion rate in repeat regions across different combinations of three technologies. Fig. S22. True CSV (DEL+INV) example at chr5:148,170,966-148,177,603 a-c, Dotplots show the comparisons of sequence between GRCh38 and GRCh38, GRCh38 and paternal haplotype, as well as GRCh38 and maternal haplotype at this locus. d, IGV snapshot shows the alignments of haplotype-resolved assemblies, HiFi reads, and Illumina reads at this locus. Fig. S23. True inversion example at chr4:87,913,966-87,950,107. Fig. S24. Tandem duplication were reported as CSV at chr1:206,046,625-206,065,379. Fig. S25. Unsure CSV in repeat regions at chr16:1,222,853, 1,261,292. Fig. S26. Complex SVs and inversions in benchmarks. Fig. S27. Recurrent inversion at chr7:40,838,845-40,841,845. Fig. S28. Violin plot shows the frequency of inversion in the HGSVC dataset. Fig. S29. F-scores of initial variants compared to the v2.0 benchmark of Chinese Quartet twin daughters. ILM_GB means the Illumina callset of the Chinese Quartet twin we obtain from the published paper (10.1186/s13059-021-02569-8). Fig. S30. Bar plots show the percentage of technology specific calls in v2.0 benchmark. Fig. S31. Variant features in different types of regions. Fig. S32. Benchmark evaluation of Chinese Quartet twin daughters. Fig. S33. The density plots show the difference in variant characteristics between high-confidence and technology-specific calls. Fig. S34. Variant distribution of Chinese Quartet at the telomere. Fig. S35. Variant distribution of Chinese Quartet at telomere and centromere. Fig. S36. STR/VNTR distribution and variant breakpoint correlation. Fig. S37. Diagram for benchmark utility. Fig. S38. IGV snapshot shows Chinese Quartet twins’ assemblies to GRCH38 in xMHC regions.