Sequencing Summary Report 0001_0115_01A

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Authors
  1. Pittet, V.
Corporate Authors
Defence Research and Development Canada, Suffield Research Centre, Ralston AB (CAN)
Abstract
Of the fourteen samples, quantifiable DNA concentrations were obtained from the extractions of samples 1-6 (Table 1). Upon PCR amplification, sample 7 provided a visible PCR amplicon, however, samples 8-14 did not. Despite low DNA concentrations, library preparation was performed for all 14 samples on the approval of DRDC, and yielded ~1,698 to 440,640 reads per sample (Table 1). As expected, samples 8-14 that did not show strong amplification by PCR produced lower read numbers (1,609 – 3,821 reads) than samples 1 – 7 which had good amplification (220,345 – 440,645 reads). The DNA extraction (RO) and PCR controls also produced reads, but in low numbers (1,1211 and 824, respectively) with only ~40% retained after quality filtering. These control samples are useful when interpreting the results in the OTU tables, and it is advised that the DNA extraction and PCR controls be considered as background noise that could also be present in other samples, especially samples 8-14 which had low PCR amplification yield and fewer reads. The number of reads in each sample matching the 16S rRNA gene from B. atrophaeus based on 97, 98, 99 or 100% identity thresholds is provided in Table 2 both as absolute and relative abundance. The samples with the highest relative abundance of sequences matching B. atrophaeus were samples 9 and 11. This abundance is largely attributed to the OTU ‘denovo335’ which was classified to the Bacillus subtilis group. The sample with the highest diversity
Keywords
DNA Sequencing;limit of detection
Report Number
DRDC-RDDC-2015-C238 — Contract Report
Date of publication
01 Jan 2015
Number of Pages
10
DSTKIM No
CA041177
CANDIS No
802536
Format(s):
Electronic Document(PDF)

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