Table 1.
Summary of data used in this study. Characteristics of these data for the Charolais trio are described here, and in more detail in this manuscript. For information about pipeline used in this study, refer to Fig. 2.
| Sample | Sequencing platform | Instrument/mode | Quantity | Insert size (bp) | Read length (bp) | Number of Gbases | Sequence depth X | ID | Pipeline use |
|---|---|---|---|---|---|---|---|---|---|
| Heifer | Oxford Nanopore | GridION/ PromethION | 3 flowcells GridIONs - 2 flowcells PromethION | NA | 25000 to 45000 | 154 | 52 | ERR10386215 to ERR10386219 | a |
| Heifer | Illumina | NovaSeq | 2 lanes S4 | 800 | 2 × 250 bp PCR Free | 337 | 112 | ERR10310239, ERR10310240 | a, c |
| Heifer | PacBio | Sequel II | 1 smrtcells CLR | NA | 100000 | 278 | 42 | ERR10378053 | a |
| Heifer | PacBio | Sequel II | 5 smrtcells CCS | NA | 15000 to 20000 | 119 | 40 | ERR10378054 to ERR10378058 | c, d |
| Heifer | Hi-C | NovaSeq/HiSeq 3000 | 1 lane SP + 1 lane HiSeq | 434 | 2 × 150 bp | 75/sample | 25/sample | ERR10310241, ERR10310244 | a, c |
| Trio | Chromium 10X | NovaSeq /MiSeq | 1 lane S4/ 1 run MiSeq | 500 | 2 × 150 bp | 267/sample | 89/sample | heifer: ERR10310247 ERR10310250 father: ERR10310248 ERR10310251 mother: ERR10310249 ERR10310252 | a, b, c |