Table 3.

Characters and efficiency comparison between the genotyping by sequencing (GBS) and the hybridization capture sequencing (HCS) for next generation sequencing enabled high throughput sugarcane genotyping (M: million)

	GBS	HCS
Clean reads (M)/uniquely mapped reads (M) (%)	54.0/17.4 (32.2%)	411.7/304.0 (73.8%)
Uniquely mapped reads in genic regions (M) (%)	14.5 (83.3%)	277.4 (67.4%)
Uniquely mapped reads in inter-genic regions (M) (%)	2.9 (16.7%)	143.4 (32.6%)
Coverage for sorghum genome (Mb) (%)	4.1 (0.6%)	115.8 (17.6%)
Coverage for genic regions (Mb) (%)	3.0 (73.2%)	70.5 (58.4%)
Coverage for inter-genic regions (M) (%)	1.1(26.8%)	45.3 (39.1%)
Total SNPs/density of coverage (per Mb)	20,691/5046.6	884,287/7636.2
SNPs in genic regions (%) /intergenic regions (%)	17,550 (84.8%)/3141 (15.2%)	799,950 (90.5%)/84,337 (9.5%)
Cost per sample/cost per thousand SNPs	$388/$0.4	$70/$3.4