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Table 7 Mapping of the amplicon sequences to associated genome references

From: Comparison of the performance of an amplicon sequencing assay based on Oxford Nanopore technology to real-time PCR assays for detecting bacterial biodefense pathogens

Organism

Strain

PCR Assay

Amplicon Length (bps)

CIGAR*

Insertions

Deletions

SC left

SC right

Alignment Expected?

Expected PCR result

Observed PCR Result

B. anthracis

708

PRC_01

110

70M3D40M

0

3

0

0

Y

+

+

B. anthracis

708

PRC_04

182

155M4D27M

0

4

0

0

Y

+

+

B. anthracis

708

PRC_07

96

96 M

0

0

0

0

Y

+

+

Y. pestis

113

PRC_09

68

68 M

0

0

0

0

Y

+

+

Y. pestis

114

PRC_09

68

68 M

0

0

0

0

Y

+

+

Y. pestis

113

PRC_11

79

79 M

0

0

0

0

Y

+

+

Y. pestis

114

PRC_14

103

103 M

0

0

0

0

Y

+

Y. pestis

113

PRC_15

67

67 M

0

0

0

0

Y

+

+

Y. pestis

114

PRC_15

67

67 M

0

0

0

0

Y

+

+

F. tularensis

239

PRC_23

135

135 M

0

0

0

0

Y

+

+

F. tularensis

240

PRC_23

135

135 M

0

0

0

0

Y

+

+

F. tularensis

241

PRC_23

135

133M2S

0

0

0

2

Y

+

+

F. tularensis

239

PRC_28

171

90M1D81M

0

1

0

0

Y

+

+

F. tularensis

239

PRC_29

119

48S71M

0

0

48

0

N

F. tularensis

240

PRC_29

119

119 M

0

0

0

0

Y

+

F. tularensis

241

PRC_29

119

71M48S

0

0

0

48

N

F. tularensis

241

PRC_30

126

126 M

0

0

0

0

Y

+

+

B. mallei

164

PRC_49

100

100 M

0

0

0

0

Y

+

+

B. pseudomallei

197

PRC_49

100

no alignment**

+

B. pseudomallei

197

PRC_50

115

115 M

0

0

0

0

Y

+

+

B. pseudomallei

197

PRC_65

67

67 M

0

0

0

0

Y

+

+

  1. Mapping of the amplicon sequences to the whole genome de novo sequence reference of the spiked strains to detect possible mismatches. All amplicon alignments match expected contig reference, however there are alignments with heavy soft clipping (SC). *Concise Idiosyncratic Gap Alignment Report; S - soft clipping, M - match, D - deletion, I - insertion. Soft-clipped parts of query sequence are ignored when calculating alignment mapping quality (consequence of local alignment). **Shown for completeness and comparison purposes