Table 4.

Evaluation analysis of variant calling, using DeepVariant tool, using read mapping results of three different types of sequencing data, short reads, ultra-long reads, and accurate long reads.

	Short reads	Ultra-long reads	Accurate long reads
Variant calling tool	DeepVariant	PEPPER + DeepVariant	DeepVariant
Version	1.3.0	0.8	1.3.0
Total number of bases in input SAM file	250,103,434,512	56,958,985,752	23,944,354,059
Phase 1 (make examples) CPU Time (sec)	250,359	1,136,356	230,066
Phase 2 (call variants) CPU Time (sec)	473,962	3,480,419	549,272
Phase 3 (post-process variants) CPU Time (sec)	2,193	2,765	6,201
Total Run Time (sec)	746,514	4,619,540	785,539
Number of Called Variants (PASS)	4,644,980	6,054,168	4,589,024
Number of Called Variants (RefCall)	1,313,292	6,722,265	2,603,968
Variant Calling Throughput (Number of called variants / sec)	7.9 variants/sec	2.77 variants/sec	9.2 variants/sec