Table 1.
Sequencing and alignment summary.
| Sample ID | Experimental Group | Input Reads | Number Uniquely Mapped Reads | Percent Uniquely Mapped Reads | Number Multi-mapped Reads | Percent Multi-mapped Reads |
|---|---|---|---|---|---|---|
| No SCI, Replicate 1 | No SCI | 43,326,516 | 38,768,226 | 89.48% | 3,919,395 | 9.05% |
| No SCI, Replicate 2 | No SCI | 42,009,023 | 37,683,145 | 89.70% | 3,696,445 | 8.80% |
| No SCI, Replicate 3 | No SCI | 48,402,602 | 43,255,174 | 89.37% | 4,415,622 | 9.12% |
| No SCI, Replicate 4 | No SCI | 41,481,052 | 37,178,297 | 89.63% | 3,677,565 | 8.87% |
| Contusion SCI, Replicate 1 | CONT SCI | 53,820,128 | 48,151,362 | 89.47% | 4,869,590 | 9.05% |
| Contusion SCI, Replicate 2 | CONT SCI | 43,710,401 | 39,145,156 | 89.56% | 3,916,247 | 8.96% |
| Contusion SCI, Replicate 3 | CONT SCI | 45,022,848 | 40,431,294 | 89.80% | 3,959,183 | 8.79% |
| Contusion SCI, Replicate 4 | CONT SCI | 43,823,672 | 38,905,291 | 88.78% | 4,201,196 | 9.59% |
| Contusion SCI, Replicate 5 | CONT SCI | 52,408,086 | 46,977,110 | 89.64% | 4,670,237 | 8.91% |
| Contusion SCI, Replicate 6 | CONT SCI | 46,302,615 | 41,341,860 | 89.29% | 4,288,060 | 9.26% |
| Contusion SCI + SWIM, Replicate 1 | CONT SCI + SWIM | 36,127,931 | 32,173,451 | 89.05% | 3,332,163 | 9.22% |
| Contusion SCI + SWIM, Replicate 2 | CONT SCI + SWIM | 22,839,371 | 20,305,455 | 88.91% | 2,142,968 | 9.38% |
| Contusion SCI + SWIM, Replicate 3 | CONT SCI + SWIM | 28,375,965 | 25,194,580 | 88.79% | 2,725,712 | 9.61% |
| Contusion SCI + SWIM, Replicate 4 | CONT SCI + SWIM | 42,055,999 | 37,629,717 | 89.48% | 3,803,462 | 9.04% |
| Contusion SCI + SWIM, Replicate 5 | CONT SCI + SWIM | 38,057,288 | 34,067,887 | 89.52% | 3,434,860 | 9.03% |
| Contusion SCI + SWW, Replicate 1 | CONT SCI + SWW | 40,038,442 | 35,829,624 | 89.49% | 3,570,182 | 8.92% |
| Contusion SCI + SWW, Replicate 2 | CONT SCI + SWW | 42,440,037 | 37,813,748 | 89.10% | 3,856,836 | 9.09% |
| Contusion SCI + SWW, Replicate 3 | CONT SCI + SWW | 33,579,211 | 30,036,726 | 89.45% | 3,034,375 | 9.04% |
| Contusion SCI + SWW, Replicate 4 | CONT SCI + SWW | 28,272,049 | 25,189,625 | 89.10% | 2,587,998 | 9.15% |
| Contusion SCI + SWW, Replicate 5 | CONT SCI + SWW | 40,461,103 | 36,117,639 | 89.27% | 3,654,807 | 9.03% |
| Complete transection SCI, Replicate 1 | TX SCI | 28,777,268 | 25,745,615 | 89.47% | 2,586,418 | 8.99% |
| Complete transection SCI, Replicate 2 | TX SCI | 41,441,568 | 36,698,047 | 88.55% | 3,981,651 | 9.61% |
| Complete transection SCI, Replicate 3 | TX SCI | 54,780,102 | 48,712,719 | 88.92% | 5,230,406 | 9.55% |
| Complete transection SCI, Replicate 4 | TX SCI | 39,452,986 | 34,821,163 | 88.26% | 3,857,604 | 9.78% |