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Table 2 Metagenomic samples used as positive controls

From: HOPS: automated detection and authentication of pathogen DNA in archaeological remains

ID

Reconstructed Bacteria

Sequencing reads

Data type

Detected

Reference

10C

Salmonella enterica

1,017,400

Shotgun

HP, KA, MB, MI, SP

[25]

35C

Salmonella enterica

986,908

Shotgun

HP, KA, MI, SP

[25]

RK1001.C0101

Yersinia pestis

7,023,370

Shotgun

HP, KA, MI, SP

[17]

GEN_72

Yersinia pestis

7,663,408

Shotgun

HP, KA, MB, SP

[17]

549_O

Yersinia pestis

1,520,471

Shotgun

HP, KA, MI, SP

[16]

JK3031UDG

Yersinia pestis

4,059,016

Shotgun (UDG)

HP, KA, MI, SP

[16]

JK2370UDG

Yersinia pestis

52,858,027

Shotgun (UDG)

HP, KA, MB, MI, SP

[16]

RT6

Yersinia pestis

6,706,316

Shotgun (UDG)

HP, KA

[18]

1343UnTal85

Yersinia pestis

3,462,216

Shotgun

HP, KA, MB, MI, SP

[17]

6Post

Yersinia pestis

2,546,695

Shotgun

HP, KA, MB, MI, SP

[17]

KunilaII

Yersinia pestis

1,007,417

Shotgun

HP, KA, MB, MI, SP

[17]

RISE00

Yersinia pestis

6,000,000

Shotgun

HP, KA, MI, SP

[13]

RISE139

Yersinia pestis

6,000,000

Shotgun

HP, KA, MB, MI, SP

[13]

RISE386

Yersinia pestis

6,000,000

Shotgun

HP, KA, MI, SP

[13]

RISE397

Yersinia pestis

6,000,000

Shotgun

HP, KA, SP

[13]

RISE505

Yersinia pestis

6,000,000

Shotgun

HP, KA, MB, MI, SP

[13]

RISE509

Yersinia pestis

6,000,000

Shotgun

HP, KA, MB, MI, SP

[13]

RISE511

Yersinia pestis

6,000,000

Shotgun

HP, KA, SP

[13]

54

Mycobacterium tuberculosis

70,897

Shotgun

HP, KA, MI, SP

[21]

58

Mycobacterium tuberculosis

114,555

Shotgun

HP, KA, MI, SP

[21]

64

Mycobacterium tuberculosis

160,310

Shotgun

HP, KA, MB, MI, SP

[21]

54

Mycobacterium tuberculosis

5,000,000

Capture (UDG)

HP, KA, MB, MI, SP

[21]

58

Mycobacterium tuberculosis

5,000,000

Capture (UDG)

HP, KA, MB, MI, SP

[21]

64

Mycobacterium tuberculosis

5,000,000

Capture (UDG)

HP, KA, MB, MI, SP

[21]

P1P2

Helicobacter pylori

5,000,000

Capture (UDG)

HP, KA, MB, MI, SP

[27]

  1. HP HOPS, KA KRAKEN, MB metaBIT, MI MIDAS, SP SPARSE