Skip to main content

Table 1 Sample statistics and read assignments

From: In silico analyses of metagenomes from human atherosclerotic plaque samples

Patients

Platform

Sample ID-DNA

Raw reads

Non-Hg19 reads

Non-Hg19 (%)

RapSearch processed (as in MEGAN)

Assigned in MEGAN (MSc:50 MSp25 MinCompl:0.44 and paired protocol)

Bacteria

% Bacteria

Cases

Hiseq 2000

48

93,124,682

31,504,036

33.83

8,404,029

3,763,197

243,336

2.90 %

Hiseq 2000

49

101,840,018

53,068,718

52.11

12,405,108

6,772,304

436,463

3.52 %

Hiseq 2000

50

94,765,328

43,109,046

45.49

11,643,905

6,419,975

505,239

4.34 %

Hiseq 2000

51

112,426,390

50,653,838

45.06

10,711,699

4,899,567

216,511

2.02 %

Hiseq 2000

52

88,328,470

36,795,952

41.66

10,574,678

5,766,665

492,013

4.65 %

Hiseq 2000

53

124,000,764

41,858,084

33.76

10,057,354

4,676,002

243,775

2.42 %

Hiseq 2000

54

93,124,682

82,366,266

88.45

19,199,623

9,229,157

365,993

1.91 %

Hiseq 2000

237

141,334,092

58,853,792

41.64

6,946,473

3,854,397

249,369

3.59 %

Hiseq 2000

238

153,302,968

36,976,828

24.12

5,216,154

3,002,923

835,412

16.02 %

Hiseq 2000

239

154,652,444

48,177,200

31.15

5,643,923

3,045,461

222,363

3.94 %

Hiseq 2000

240

101,591,496

46,000,276

45.28

5,166,877

2,640,033

110,186

2.13 %

Hiseq 2000

241

99,927,824

42,032,952

42.06

4,607,355

2,471,259

153,425

3.33 %

Hiseq 2000

242

82,850,664

46,721,284

56.39

5,002,916

2,716,756

135,617

2.71 %

Hiseq 2000

243

104,094,892

52,853,464

50.77

5,726,930

3,095,542

193,819

3.38 %

Hiseq 2500

977 (P0613)

111,699,176

13,191,406

11.81

2,344,220

955,602

74,646

3.18 %

Miseq V1

P0613 repeat

7,184,184

980,004

13.64

759,262

228,262

31,889

4.20 %

 

977 + APD1

118,883,360

14,171,410

11.92

3,103,482

1,183,864

106,535

3.43 %

Controls

Hiseq 2000

55

105,779,932

29,019,712

27.43

8,911,853

4,040,359

293,160

3.29 %

Hiseq 2000

56

128,471,814

10,767,822

8.38

4,680,735

1,922,688

204,397

4.37 %

Hiseq 2000

232

127,173,774

25,793,632

20.72

3,267,969

1,726,714

164,711

5.04 %

Hiseq 2000

233

166,547,592

29,282,304

17.58

4,559,468

2,634,338

649,226

14.24 %

Hiseq 2000

234

114,673,124

37,683,568

32.86

4,550,457

2,477,740

193,659

4.26 %

Hiseq 2000

235

151,195,284

34,767,160

22.99

4,633,661

2,550,975

231,926

5.01 %

Hiseq 2000

236

152,179,180

32,269,700

21.21

4,254,572

2,319,403

204,778

4.81 %

Total

  

2,610,268,774

685,143,146

26.25

   

4.60 %

  1. Details of sample information, sequencing read statistics, and assignments of reads after different stages of data processing