Table 3.
Summary of Elephant Whole-Genome Shotgun Resequencing Data Utilized in This Study, Mapped to the African Bush Elephant Reference Assembly (loxAfr3.0).
| Species | Name | Geographic Origin | Source | No. Mapped Reads | Prop. Reads Properly Paired | Peak Read Depth |
|---|---|---|---|---|---|---|
| Loxodonta africana | Watoto | Kenya | ERR2260496 | 874,537,386 | 0.99 | 26× |
| Swazi | South Africa | ERR2260497 | 1,014,067,450 | 0.93 | 30× | |
| Hi-Dari | Kenya | SRR11869865, SRR11869866,(Current study) | 1,072,817,612 | 0.97 | 38× | |
| Christie | Zimbabwe | SRR12799664, SRR12799663 (Current study; Abegglen et al. 2015) |
1,031,044,341 | 0.98 | 36× | |
| Loxodonta cyclotis | DS1546 | Central African Republic | ERR2260495 | 852,948,500 | 0.96 | 24× |
| Coco | Sierra Leone | ERR2260500 | 981,145,080 | 0.99 | 30× | |
| Elephas maximus | Moola | Myanmar | ERR2260498 | 1,188,021,033 | 0.99 | 36× |
| Chendra | Borneo | ERR2260499 | 981,228,188 | 0.99 | 30× | |
| Icky | Myanmar | SRR11577048 (Current study) |
898,020,572 | 0.97 | 32× | |
| Parvathy | India | SRR2008170 | 872,535,345 | 0.96 | 26× | |
| Asha | India | SRR2009586 | 977,136,495 | 0.94 | 29× | |
| Uno | Assam, India | SRR2012205, SRR2012206, SRR2012207 | 912,606,191 | 0.96 | 26× | |
| Jayaprakash | Karnataka, India | SRR2912975 | 475,023,505 | 0.94 | 13× | |
| Palaeoloxodon antiquus | NA | Germany | ERR2260504 | 916,662,984 | NA | 7× |
| Mammuthus primigenius | NA | Oimyakon, Russia | ERR852028 | 617,446,606 | NA | 10× |
| NA | Wrangel Island, Russia | ERR855944 | 760,223,385 | NA | 16× |