Table 2. Analysis of association between mutation events and tandem-repeat or low-complexity DNA regions.
| Mutation type | Parasite line | Number | Mean TR content (%) | Different from whole genome? | Different from 3D7 WT? | Mean LCR content (%) | Different from whole genome? | Different from 3D7 WT? |
|---|---|---|---|---|---|---|---|---|
| S.V. | 3D7 WT | 44 | 17.9 | N (p = 0.229) | 19.3 | Marginal (p = 0.014) | ||
| ΔPfBLM | 77 | 19.1 | N (p = 0.068) | N (p = 0.848) | 13.6 | Y (p < 0.001) | N (p = 0.195) | |
| PfWRN-k/d | 298 | 17.8 | Y (p < 0.001) | N (p = 0.976) | 12.1 | Y (p < 0.001) | N (p = 0.053) | |
| indel | 3D7 WT | 43 | 19.3 | Y (p = 0.009) | 40.0 | Y (p = 0.006) | ||
| ΔPfBLM | 32 | 21.2 | Y (p = 0.006) | N (p = 0.653) | 37.6 | Y (p < 0.001) | N (p = 0.577) | |
| PfWRN-k/d | 96 | 15.8 | Y (p < 0.001) | N (p = 0.219) | 38.8 | Y (p < 0.001) | N (p = 0.700) | |
| SNP | 3D7 WT | 11 | 20.9 | N (p = 0.152) | 32.8 | N (p = 0.517) | ||
| ΔPfBLM | 10 | 20.4 | N (p = 0.484) | N (p = 0.967) | 9.6 | Y (p = 0.003) | Marginal (p = 0.013) | |
| PfWRN-k/d | 13 | 12.8 | N (p = 0.819) | N (p = 0.248) | 18.3 | Marginal (p = 0.021) | N (p = 0.088) | |
| Whole genome | 23287 | 12 | 28.1 | |||||
| ORFs only | 5602 | 7.8 | 19.5 |
For each type of mutation in each parasite line, the table shows the mean percentage of tandem-repeat (TR) or low-complexity (LCR) DNA in the 1kb surrounding each mutation. Significant differences between these percentages and the whole-genome average (calculated from 1kb windows across the whole genome) were assessed by 2-tailed t-test. The average TR/LCR content of all genomic ORFs was also calculated, for comparison with the whole-genome average, and as expected ORFS contained a lower percentage of TRs/LCRs.