Table 1.
Sequence variation in 40 + 1 rat strains
| Rat strain | Publication | PMID | Sequencing platform | Number of SNVs | Number of indels | Number of structural variants |
|---|---|---|---|---|---|---|
| ACI/EurMcwi | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,539,775 | 1,651,251 | 7,259 |
| ACI/N | Baud et al. | 23708188 | SOLiD 4 and 5500 | 3,125,523 | 1,382,793 | 19,541 |
| BBDP/Wor | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,279,444 | 1,526,223 | 3,678 |
| BN/SsN | Baud et al. | 23708188 | SOLiD 4 and 5500 | 59,402 | 660,918 | 14,126 |
| BN-Lx/Cub | Simonis et al.; Atanur et al. | 22541052; 23890820 | SOLiD 2,3 and 4 | 102,359 | 627,056 | 13,391 |
| BN-Lx/CubPrin | Hermsen et al. | na | Illumina HiSeq2000 | 140,376 | 420,433 | 13,410 |
| BUF/N | Baud et al. | 23708188 | SOLiD 4 and 5500 | 2,848,992 | 1,302,710 | 18,481 |
| DA/BklArbNsi | Guo et al. | 23695301 | Illumina HiSeq2000 | 3,368,008 | 1,567,160 | 4,184 |
| F334/N | Baud et al. | 23708188 | SOLiD 4 and 5500 | 2,947,509 | 1,342,709 | 20,881 |
| F344/NCrl | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,369,205 | 1,579,418 | 3,492 |
| F344/NHsd | Guo et al. | 23695301 | Illumina HiSeq2000 | 3,367,166 | 1,573,573 | 3,950 |
| FHH/EurMcwi | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,389,304 | 1,592,915 | 3,011 |
| FHL/EurMcwi | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,361,824 | 1,586,543 | 8,504 |
| GK/Ox | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,549,952 | 1,575,619 | 4,241 |
| LE/Stm (Illumina) | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,412,610 | 1,578,099 | 2,598 |
| LE/Stm (SOLiD) | Baud et al. | 23708188 | SOLiD 4 and 5500 | 2,949,814 | 1,359,947 | 21,038 |
| LEW/Crl | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 2,884,477 | 1,409,659 | 3,642 |
| LEW/NCrl | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 2,884,763 | 1,402,459 | 3,996 |
| LH/MavRrrc | Atanur et al.; Ma et al. | 23890820; 24628878 | Illumina HiSeq2X00 | 3,369,852 | 1,584,236 | 2,891 |
| LL/MavRrrc | Atanur et al.; Ma et al. | 23890820; 24628878 | Illumina HiSeq2X00 | 3,329,343 | 1,565,343 | 3,070 |
| LN/MavRrrc | Atanur et al.; Ma et al. | 23890820; 24628878 | Illumina HiSeq2X00 | 3,319,381 | 1,562,698 | 2,952 |
| M520/N | Baud et al. | 23708188 | SOLiD 4 and 5500 | 2,896,825 | 1,321,431 | 19,308 |
| MHS/Gib | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,183,312 | 1,513,330 | 2,917 |
| MNS/Gib | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,168,796 | 1,538,413 | 3,105 |
| MR/N | Baud et al. | 23708188 | SOLiD 4 and 5500 | 2,878,806 | 1,350,411 | 18,001 |
| SBH/Ygl | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,393,610 | 1,617,252 | 14,787 |
| SBN/Ygl | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,300,171 | 1,592,247 | 15,216 |
| SHR/NCrlPrin | Hermsen et al. | na | Illumina HiSeq2000 | 3,736,435 | 1,694,012 | 14,179 |
| SHR/NHsd | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,756,155 | 1,705,126 | 3,950 |
| SHR/OlaIpcv | Simonis et al.; Atanur et al. | 22541052; 23890820 | Illumina Genome Analyser 2 | 3,747,579 | 1,706,963 | 4,066 |
| SHR/OlaIpcvPrin | Hermsen et al. | na | Illumina HiSeq2000 | 3,709,362 | 1,689,758 | 14,069 |
| SHRSP/Gla | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,700,495 | 1,723,961 | 2,301 |
| SR/Jr | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,353,579 | 1,568,778 | 3,699 |
| SS/Jr | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,311,117 | 1,553,050 | 3,685 |
| SS/JrHsdMcwi | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,310,209 | 1,595,799 | 7,938 |
| SUO_F344 | Hermsen et al. | na | Illumina HiSeq2000 | 3,349,024 | 1,549,272 | 11,864 |
| WAG/Rij | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,092,505 | 1,485,673 | 3,650 |
| WKY/Gla | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,777,400 | 1,725,868 | 3,292 |
| WKY/N | Baud et al. | 23708188 | SOLiD 4 and 5500 | 3,213,913 | 1,419,460 | 21,832 |
| WKY/NCrl | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,502,459 | 1,700,646 | 3,630 |
| WKY/NHsd | Atanur et al. | 23890820 | Illumina HiSeq2X00 | 3,682,736 | 1,665,949 | 4,691 |
| WN/N | Baud et al. | 23708188 | SOLiD 4 and 5500 | 2,899,096 | 1,323,116 | 18,995 |
Sequence information from 40 known strains was used. The unknown SUO_F344 strain was also included in the analysis. In addition LE/Stm was sequenced with two separate sequencing platforms: Illumina and SOLiD; these two datasets were treated as separate samples in the analysis. Therefore in total this table contains variant information of 42 samples from 40 + 1 rat strains.