Table 2 Salmonella analyses.

From: Monitoring the microbiome for food safety and quality using deep shotgun sequencing

Salmonella-positive sample

k-mer classification

Whole-genome alignment

ef-Tu alignment

MFMB-04

8th

10th

1st

MFMB-20

9th

9th

4th

MFMB-38

20th

3rd

21st

MFMB-41

30th

6th

28th

Rank-sum test P value

P = 0.86

P = 0.06

P = 0.56

  1. The ranks for Salmonella-positive samples and the associated P values from Wilcoxon rank-sum test are shown for high-throughput sequencing read abundance (in RPM) for multiple analyses: k-mer classification to NCBI Microbial RefSeq Complete (left), alignments to 1447 Salmonella genomes (middle), and alignments to 4846 ef-Tu gene sequences (right). The corresponding Salmonella relative abundances are shown in Fig. 7a–c.
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