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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