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Exact(8)
Our results suggested that most of the test loci were truly CNVs.
Of these, 662 (76%) amplified reliably at a minimum of three of four test loci and were thus genotyped at an additional 11 loci.
PCR amplification of the two test loci were performed at least twice for each enzyme tested and in each case the same results were obtained.
A total of 885 scans (77% of the total) resulted in at least one of three test loci being detected with genome-wide significance, while 316 scans (27% of the total) resulted in at least suggestive significance at all three test loci.
We first used this information to estimate the substitution rate for each of the test loci in BEAST using a reduced data set of both species and Cheirogaleus (see Additional file 1: Table S1).
As was expected from previous phylogenetic evaluations [ 1, 3, 7], each of the test loci were found to be intact in the Ghana collection PGG2 M. tuberculosis strains, excepting TbD1.
Similar(52)
The copy number of the test locus in each case was defined as 2T−ΔΔC where ΔCT is the difference in threshold cycle number for the test and reference loci.
The copy number of the test locus is then estimated from the ratio of test to reference products.
The two amplicons are distinguished by size, and their relative product amounts used to determine the test locus copy number.
CT values were determined for test and reference reactions in each sample, averaged, and subtracted to obtain deltaCT (dCT) [dCT = CT (test locus) – CT (reference locus)].
The peak areas were extracted using GeneMapper software (Applied Biosystems) and the ratio of test locus to reference locus was calculated for each sample.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com