Table 1. Study overview.
| Sample | Published in | Low QC | Celera | Celera & Y | Y | Contami-nation | Remaining |
|---|---|---|---|---|---|---|---|
| ACI/EurMcwi | Atanur, S. et al. (2013) | 39% | 39% | 0% | 1% | 0% | 21% |
| BBDP/Wor | Atanur, S. et al. (2013) | 38% | 44% | 0% | 0% | 0% | 18% |
| BN-Lx/CubPrin | Hermsen, R. et al. (2015) | 41% | 42% | 2% | 1% | 0% | 14% |
| DA/BklArbNsi | Guo, X. et al. (2013) | 40% | 26% | 11% | 5% | 3% | 15% |
| F344/NCrl | Atanur, S. et al. (2013) | 39% | 40% | 0% | 2% | 0% | 18% |
| F344/NHsd | Guo, X. et al. (2013) | 40% | 26% | 13% | 6% | 1% | 13% |
| SUO_F344 | Hermsen, R. et al. (2015) | 39% | 40% | 2% | 1% | 0% | 17% |
| F344/Stm # | Unpublished | 44% | 27% | 0% | 0% | 0% | 30% |
| FHH/EurMcwi | Atanur, S. et al. (2013) | 41% | 40% | 0% | 1% | 0% | 18% |
| FHL/EurMcwi | Atanur, S. et al. (2013) | 44% | 36% | 0% | 1% | 0% | 19% |
| GK/Ox | Atanur, S. et al. (2013) | 43% | 34% | 1% | 3% | 0% | 19% |
| LE/Stm | Atanur, S. et al. (2013) | 36% | 31% | 10% | 8% | 6% | 9% |
| LEW/Crl | Atanur, S. et al. (2013) | 39% | 40% | 0% | 2% | 0% | 19% |
| LEW/NCrlBR | Atanur, S. et al. (2013) | 39% | 35% | 0% | 1% | 7% | 18% |
| LH/MavRrrc | Atanur, S. et al. (2013) | 42% | 38% | 0% | 1% | 0% | 18% |
| LL/MavRrrc | Atanur, S. et al. (2013) | 41% | 40% | 0% | 1% | 0% | 17% |
| LN/MavRrrc | Atanur, S. et al. (2013) | 42% | 39% | 0% | 1% | 0% | 17% |
| MHS/Gib | Atanur, S. et al. (2013) | 43% | 40% | 0% | 0% | 0% | 17% |
| MNS/Gib | Atanur, S. et al. (2013) | 43% | 40% | 0% | 0% | 0% | 17% |
| SBH/Ygl | Atanur, S. et al. (2013) | 34% | 45% | 0% | 1% | 0% | 20% |
| SBN/Ygl | Atanur, S. et al. (2013) | 49% | 35% | 0% | 1% | 0% | 15% |
| SHR/OlaIpcv | Atanur, S. et al. (2010) | 35% | 31% | 8% | 8% | 8% | 9% |
| SHR/NCrlPrin | Hermsen, R. et al. (2015) | 38% | 41% | 2% | 1% | 0% | 17% |
| SHR/NHsd | Atanur, S. et al. (2013) | 39% | 40% | 0% | 2% | 0% | 20% |
| SHR/OlaIpcvPrin * | Hermsen, R. et al. (2015) | 38% | 42% | 2% | 1% | 0% | 17% |
| SHRSP/Gla | Atanur, S. et al. (2013) | 45% | 33% | 0% | 1% | 3% | 17% |
| SR/Jr | Atanur, S. et al. (2013) | 40% | 38% | 0% | 1% | 0% | 21% |
| SS/Jr | Atanur, S. et al. (2013) | 40% | 37% | 0% | 1% | 0% | 21% |
| SS/JrHsdMcwi | Atanur, S. et al. (2013) | 33% | 46% | 0% | 1% | 0% | 19% |
| WAG/Rij | Atanur, S. et al. (2013) | 43% | 24% | 0% | 0% | 0% | 33% |
| WKY/Gla | Atanur, S. et al. (2013) | 39% | 41% | 0% | 2% | 0% | 18% |
| WKY/NCrl | Atanur, S. et al. (2013) | 40% | 39% | 0% | 1% | 0% | 19% |
| WKY/NHsd | Atanur, S. et al. (2013) | 49% | 17% | 0% | 1% | 0% | 33% |
Analyzed strains and the origins of unmapped reads in percentages
* Illumina GAII sequencing platform
# Mate-pair library