Skip to main content

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 %