Table 4.
Detailed classification results on five human-captured mouse exomes from different mouse strains ( A/J, BALB/c, C57BL/6)
| A/J-1 | xengsort | xenome | XfR | |||
|---|---|---|---|---|---|---|
| Time | 70 Cm | 14 Wm | 371 Cm | 45 Wm | 56 Cm | 56 Wm |
| Fragmets | (%) | Fragmets | (%) | Fragmets | (%) | |
| Mouse | 46,648,014 | (78.03) | 45,759,814 | (76.54) | ||
| Both | 120,808 | (0.20) | 65,269 | (0.11) | ||
| Human | 12,813,583 | (21.43) | 12,500,844 | (20.91) | 6,315,955 | (10.56) |
| Ambgs. | 58,449 | (0.10) | 1,383,547 | (2.31) | ||
| Neither | 143,775 | (0.24) | 75,155 | (0.13) | ||
| A/J-2 | xengsort | xenome | XfR | |||
|---|---|---|---|---|---|---|
| Time | 70 Cm | 15 Wm | 416 Cm | 50 Wm | 67 Cm | 67 Cm |
| Fragmets | (%) | Fragmets | (%) | Fragmets | (%) | |
| Mouse | 60,255,189 | (95.57) | 59,135,489 | (93.80) | ||
| Both | 151,396 | (0.24) | 89,089 | (0.14) | ||
| Human | 2,301,384 | (3.65) | 2,271,131 | (3.60) | 1,718,545 | (2.73) |
| Ambgs. | 57,827 | (0.09) | 1,340,814 | (2.13) | ||
| Neither | 279,556 | (0.44) | 208,829 | (0.33) | ||
| BALB/c | xengsort | xenome | XfR | |||
|---|---|---|---|---|---|---|
| Time | 68 Cm | 15 Wm | 392 Cm | 45 Wm | 61 Cm | 61 Wm |
| Mouse | 62,235,960 | (98.99) | 61,274,277 | (97.46) | ||
| Both | 118,541 | (0.19) | 68,949 | (0.11) | ||
| Human | 342,908 | (0.55) | 348,154 | (0.55) | 285,556 | (0.45) |
| Ambgs. | 45,063 | (0.07) | 1,098,036 | (1.65) | ||
| Neither | 127,035 | (0.20) | 80,091 | (0.13) | ||
| C57BL/6-1 | xengsort | xenome | XfR | |||
|---|---|---|---|---|---|---|
| Time | 72 Wm | 14 Wm | 359 Wm | 44 Wm | 58 Cm | 58 Wm |
| Mouse | 57,993,361 | (98.93) | 57,522,446 | (98.13) | ||
| Both | 118,984 | (0.20) | 74,325 | (0.13) | ||
| Human | 375,716 | (0.64) | 376,653 | (0.64) | 290,894 | (0.50) |
| Ambgs. | 27,731 | (0.05) | 571,542 | (0.98) | ||
| Neither | 103,895 | (0.18) | 74,721 | (0.13) | ||
| C57BL/6-2 | xengsort | xenome | XfR | |||
|---|---|---|---|---|---|---|
| Time | 67 Cm | 15 Wm | 422 Cm | 51 Wm | 62 Cm | 62 Wm |
| Mouse | 62,384,448 | (99.00) | 61,941,783 | (98.30) | ||
| Both | 107,019 | (0.17) | 66,163 | (0.10) | ||
| Human | 189,536 | (0.30) | 208,149 | (0.33) | 132,535 | (0.21) |
| Ambgs. | 27,142 | (0.04) | 562,659 | (0.89) | ||
| Neither | 304,677 | (0.48) | 234,068 | (0.37) | ||
Running times are reported both in CPU minutes (Cm), measuring CPU work, and wall clock minutes (Wm), measuring actual time spent. Times for XenofilteR (XfR) do not include alignment or BAM sorting time. Classification results report the number and percentage (in brackets) of fragments classified as mouse (correct), both human and mouse (likely correct), human (incorrect), ambiguous (no statement) and neither (likely incorrect). XenofilteR (XfR) only extracts human fragments and does not classify the remainder; so only the number of fragments classified as human are reported