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Table 1 Comparison of correct mSFP calling rates using different cut off values

From: Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

  Overall rate GC filtered Probe filtered Corrected rate
Cutoff value 7G8 Dd2 HB3 7G8 Dd2 HB3 7G8 Dd2 HB3 7G8 Dd2 HB3
1.5 92.5 92.4 90.0 92.6 92.5 90.2 93.7 93.4 91.2 97.7 97.6 96.7
2.0 91.5 90.4 89.2 91.3 90.4 89.4 92.8 92.6 90.7 97.4 97.3 96.6
5.0 82.9 82.0 82.5 82.9 82.1 82.8 86.4 85.9 84.5 95.0 94.8 94.3
  1. To obtain the best correct call rates, we compared mSFP calls using three cutoff values (1.5, 2.0, and 5.0). First we called mSFP using unique probes and probe position 3–23 (Overall rate). We repeated the calls after removing probes with GC contents < 16% and > 50% (GC filtered). We then obtained call rates after removing probes with GC content < 16% and > 50% and excluding calls with single probes and multiple probe calls with less than 75% probe votes (Probe filtered). Corrected rates were obtained after adjusting for 63.5% error rate in the wrong calls due to sequence errors, which were calculated using formula
  2. [(100-probe filtered rate) × 0.635 + probe filtered rate].
  3. A correct call was defined as correct calls over the sum of correct, wrong, and tie calls.
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