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Table 4 True CNVs detected in the Dd2 bulk genome

From: Single-cell sequencing of the small and AT-skewed genome of malaria parasites

Name Chr. Start Pos. Size (bp) Type Support read* Start Pos. Size (bp) Copy number detected by Ginkgo** in different bin sizes Mappability^
Discordant read Split read 1 kb 5 kb 8 kb 10 kb
Pfmdr1 5 888316 81,935 DUP 53 0 888000 82,000 2 2 Nd Nd 1
Pf11-1 10 1524527 18,472 DUP 29 1 1520000 28,000 4 5 N/A N/A 0.86
Pf332 11 1956623 8719 DUP 0 8 1953000 13,000 4 N/A N/A N/A 0.92
  1. *Detected by LUMPY based on discordant/split read detection, minimum number of supporting reads is 2
  2. **For Ginkgo analysis, the minimum bin number of segmentation is 5
  3. ^For comparison, the mean mappability of the core genome is 0.99 and the mean mappability telomere/subtelomere regions including var gene clusters is 0.65
  4. DUP duplication, N/A not applicable because the target CNVs will not be detected as the bin size (≥ 5× bin size) is larger than the size of the target CNVs, Nd not detected in the specified bin size