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Table 1 Sequencing quality and statistical parameters in FF, FFPE and PB samples

From: Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST)

Patient

Sample

Total n° Reads

High Quality Bases (n°)

% Trimmed Bases

Unique Reads (n°)

% PCR duplicate

n° Mapped Reads

% Mapped Reads

GIST193

FF

63,523,138

5.84E + 09

8.1 %

58,598,506

7.8 %

57,879,604

98.8 %

FFPE

54,852,570

4.97E + 09

9.4 %

49,208,829

10.3 %

48,499,561

98.6 %

PB

42,361,296

3.80E + 09

10.3 %

39,964,111

5.7 %

39,385,105

98.6 %

GIST165

FF

53,644,770

4.95E + 09

7.7 %

49,587,098

7.6 %

49,019,552

98.9 %

FFPE

50,570,884

4.59E + 09

9.3 %

45,332,397

10.4 %

44,682,820

98.6 %

PB

42,235,292

3.87E + 09

8.3 %

39,957,754

5.4 %

39,460,107

98.8 %

GIST174

FF

56,267,604

5.10E + 09

9.3 %

52,033,110

7.5 %

51,338,819

98.7 %

FFPE

64,625,134

5.87E + 09

9.2 %

58,169,850

10.0 %

57,529,198

98.9 %

PB

52,136,904

4.69E + 09

10.0 %

48,822,001

6.4 %

48,110,730

98.5 %

GIST127

FF

48,223,180

4.42E + 09

8.4 %

44,804,080

7.1 %

44,294,468

98.9 %

FFPE

14,203,932

1.14E + 09

20.7 %

12,496,962

12.0 %

12,310,812

98.1 %

PB

43,078,472

3.86E + 09

10.4 %

40,476,585

6.0 %

39,924,959

98.4 %