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
| Â | 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 |