Skip to main content

Table 1 Summary of putative and confirmed CNVs

From: High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians

 

Putative CNVs

High conf

Singleton

CBS all probes

CBS smoothed

Confirmed CNVs

Confirmed high conf

Confirmed singleton

Parent set

 

Putatives

Putatives

Putatives

Putatives

Putatives

Putative high conf

Putative singleton

Number of CNVs

6,578

3,850

2,728

5,842

736

6,368

3,799

2,569

% of parent set

 

58.5%

41.5%

88.8%

11.2%

96.8%

98.7%

94.2%

Median length

4.9 kb

5.9 kb

3.7 kb

4.0 kb

70.7 kb

4.4 kb

5.3 kb

3.1 kb

   25th percentile

1.7 kb

2.3 kb

1.1 kb

1.5 kb

48.5 kb

1.5 kb

2.1 kb

1.0 kb

   75th percentile

15.7 kb

19.0 kb

12.0 kb

9.8 kb

105.9 kb

13.2 kb

16.8 kb

9.1 kb

DGV overlap

3,780

2,587

1,193

3,346

434

3,678

2,551

1,127

% DGV

57.5%

67.2%

43.7%

57.3%

59.0%

57.8%

67.1%

43.9%

Med len in DGV

6.6 kb

7.6 kb

4.5 kb

5.2 kb

77.0 kb

5.8 kb

6.8 kb

3.9 kb

Novel CNVs

2,798

1,263

1,535

2,496

302

2,690

1,248

1,442

Med len novel

3.4 kb

3.6 kb

3.2 kb

2.8 kb

64.5 kb

3.0 kb

3.2 kb

2.6 kb

  1. Putative CNVs are regions where at least one event was observed in the initial genome scan; confirmed CNVs are a subset of putative CNVs where at least one event was observed on the CNV-typing array. 'High conf' (high confidence) refers to putative CNVs that had events observed in at least two Yoruba, while singletons are putative CNVs with observed events in only one Yoruba. 'CBS all probes' refers to putative CNVs identified in the segmentation analysis using all probes on the genome-scan arrays, while 'CBS smoothed' refers to generally longer CNVs identified in smoothed segmentation analysis. At least 5% of a CNV region was required to overlap a record from the DGV (March 2009). Med len, median length.