Table 1.
Contamination test summary
| Variant type | %Contamination | %Correct | %Fragmented | %Mismatches |
|---|---|---|---|---|
| None | 0 | 100% | 0% | 12.29% |
| 1 SNP | 20% | 100% | 0% | 13.38% |
| 35% | 96% | 0% | 14.41% | |
| 50% | 44% | 0% | 14.68% | |
| 2 SNPs | 20% | 100% | 0% | 14.35% |
| 35% | 96% | 0% | 14.82% | |
| 50% | 32% | 0% | 15.96% | |
| 3 SNPs | 20% | 100% | 0% | 14.04% |
| 35% | 96% | 0% | 15.21% | |
| 50% | 35% | 0% | 16.58% | |
| 4 SNPs | 20% | 100% | 0% | 14.85% |
| 35% | 90% | 0% | 16.83% | |
| 50% | 18% | 0% | 17.99% | |
| 608 bp indel | 10% | 99% | 1% | 13.49% |
| 20% | 89% | 11% | 14.78% | |
| 35% | 16% | 84% | 17.28% | |
| 50% | 2% | 95% | 21.00% | |
| Unrelated | 10% | 86% | 4% | 18.24% |
| 20% | 28% | 72% | 23.96% | |
| 35% | 0% | 100% | NA | |
| 50% | 0% | 100% | NA |
Each row of this table represents the average result from a single simulation experiment (repeated 500 times). Each experiment differed by the amount and type of contamination simulated. Variant Type denotes by what metric the ‘contaminating’ sequence (reads from a different sample that were artificially spiked) differs from the ‘primary’ sequence (the reference sample). %Contamination refers to the percentage of the read library derived from contaminating reads. %Correct denotes the percentage of correct assemblies yielded. %Fragmented denotes the percentage of fragmented assemblies yielded. %Mismatches denotes the percentage of assemblies that did not exactly match the reference.