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Table 2 Comparison of average sequencing quality metrics

From: A formalin-free method for stabilizing cells for nucleic acid amplification, hybridization and next-generation sequencing

 

Frozen control

SCP

p value

Total reads (×106)

24.6 ± 0.33

34.1 ± 1.86

0.01

Unique reads (×106)

2.89 ± 1.26

4.75 ± 0.63

0.23

Mapped unique reads (×106)

2.45 ± 1.11

4.15 ± 0.60

0.22

Bases on-targeta (×106)

89.8 ± 47.4

177 ± 32.16

0.19

% Bases on-target

51.3 ± 0.02

50.8 ± 0.00

0.69

Total discrepanciesb (×105)

1.17 ± 0.31

1.75 ± 0.27

0.14

Discrepancies per read

0.06 ± 0.04

0.04 ± 0.00

0.55

Number of bases <Q20c (×106)

0.77 ± 0.29

1.23 ± 0.26

0.20

Number of bases <Q20 per reads

0.46 ± 0.20

0.60 ± 0.61

0.63

Mean insert size

98 ± 5.51

119 ± 5.20

0.07

  1. aOn-target means mapping to the targets
  2. bDiscrepancies mean any base called in a read that is different from the
  3. reference sequence
  4. cQ20: Phred mapping quality score of 20
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BMC Research Notes

ISSN: 1756-0500

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