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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)

From: Mining sequence variations in representative polyploid sugarcane germplasm accessions

  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