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Table 2 Trimming, filtering, and mapping of PacBio-derived reads for error estimation

From: Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections

pError

Template HCMV DNA

Input DNA

Reference length in kb

Number and average read length of sequencing reads

     

raw reads

after qtrim

after hu removal

% of reads < 500 bases

after ltrim

% HCMV mapping

map to reference

average coverage

0.01

Merlin

amplicons

15.5

number

92,128

63,604

30,632

18.7

24,909

98.26

24,475

6885

    

length

4656

2820

3741

 

4547

   
 

TB40-BAC4-luc

amplicons

15.5

number

73,439

46,547

42,060

19.1

34,041

99.53

33,881

9062

    

length

6162

3590

3767

 

4601

   
 

Merlin

non-enriched

237

number

143,728

102,444

5166

13.9

4447

85.29

3793

45

    

length

4378

2722

2956

 

3397

   
 

TB40-BAC4-luc

non-enriched

235

number

96,966

72,804

9122

12.6

7975

93.63

7467

73

    

length

3583

2439

2417

 

2731

   

0.001

Merlin

amplicons

15.5

number

92,128

50,031

22,247

36.4

14,154

97.76

13,837

2444

    

length

4656

1631

1896

 

2843

   
 

TB40-BAC4-luc

amplicons

15.5

number

73,439

34,137

30,361

37.2

19,070

99.26

18,929

3118

    

length

6162

1814

1865

 

2828

   
 

Merlin

non-enriched

237

number

143,728

83,991

4028

27.2

2931

86.49

2535

25

    

length

4378

1849

1934

 

2566

   
 

TB40-BAC4-luc

non-enriched

235

number

96,966

60,539

7402

23.2

5688

94.57

5379

45

    

length

3583

1727

1751

 

2205

   
  1. kb, kilobases; qtrim, quality trim; hu, human DNA-specific reads; ltrim, length trim