Table 2.

Read alignment summary for exomes and RNA sequencing. Tables summarizing alignment data from exome sequencing (A) and RNA sequencing (B) of patient’s leukemia cell (Initial tumor) and normal PBMCs (Final normal)

(A)
Exome seq	Initial tumor	Final normal
Total reads after preprocessing	225,995,396	101,103,622
Total aligned reads	225,584,786 (99.82%)	100,959,910 (99.86%)
Total passed alignment	218,518,588 (96.69%)	97,739,805 (96.67%)
Total cross mapped	515,172 (0.23%)	242,189 (0.24%)
Duplicate (%)	18.9	17.4
Overall mean insert size	161.16	158.09
Overall mean mapping quality	57.68	57.7
(B)
RNA seq	Initial tumor
Total reads	176,127,016
Read count after adapter trimming	175,964,200
Read count after contamination removal	165,170,982
% Data loss	6.22
Reads aligned	161,516,678
Alignment (%)	97.79