Table 1.
Quality evaluation of RAD-seq data for parents and progeny
| Sample | Clean bases (Gb) | Clean reads (M) | Q20 (%) | Q30 (%) | GC content (%) | Coverage of genomea(X) | Depth of RAD tagsb (X) | |
|---|---|---|---|---|---|---|---|---|
| Parents | Honeycrisp | 23.31 | 76.95 | 95.38 | 89.75 | 37.42 | 31.41 | 77.75 |
| Qinguan | 20.15 | 66.93 | 93.73 | 86.91 | 38.47 | 27.16 | 72.24 | |
| Progeny | Average | 1.05 | 3.50 | 94.08 | 87.30 | 37.64 | ||
| Maximum | 3.02 | 10.07 | 96.53 | 91.75 | 40.14 | 4.07 | 23.88 | |
| Minimum | 0.52 | 1.75 | 92.55 | 85.00 | 35.78 | 0.71 | 8.76 | |
| Total | 357.15 | 1191.18 | ||||||
| All samples | 400.61 | 1335.06 | ||||||
a Coverage of genome meant the proportion of total clean bases aligned to apple reference genome accounted for the genome size. The size of apple reference genome was 742.3 Mb estimated by Velasco et al.[35]. bDepth of RAD tags meant the sequencing depth of filtered RAD tags