Fig. 2

Small variant in the twins of the Chinese Quartet. a Overlap of SNVs and indels among ILM, HiFi, and HRA, respectively. b Bar plot depicts the percentage of ILM, HiFi, and HRA calls in SNV (left) and indel (right) benchmark, with gray stripes representing the percentages of calls supported by BGI reads. c indel length distribution of indels across HG002 in GIAB (v4.2.1) and twins in Chinese Quartet. d Left bar represents the percentages of indels in seven different combinations of three technologies. Right bars represent the percentages of indels at STR regions across different combinations of three technologies. The black and red dot lines refer to the percentages of indels at STR regions in whole benchmarking set of GIAB and this study. e IGV snapshot shows a heterozygous insertion at a TCC repeat. This insertion is detected by both HRA and HiFi reads. f IGV snapshot shows a homozygous deletion at a homopolymer region. This deletion is only reported by HRA