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As this is dictated by the sample with the lowest sequence depth, we plotted the relationship of this with the number of overlap mutations and did not see any correlation (Additional file 14), suggesting it was not due the sequence depth difference but more likely caused by the degree of tumor abnormality.
The lowest sequence depth for the BRAF c.1793C to c.1807C region was 214 for the six samples (range [214 to 2246]), and the original mutational status of each sample was confirmed, excluding the possibility of additional and low-frequency mutations.
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Admittedly, LB-antibiotics has the lowest sequencing depth of all.
The samples (total and polysomal) which had the lowest sequencing depth were not affected.
Shannon diversity indices (H′) were calculated after rarefying the different data sets from the same soil to the same sequencing depth (i.e. the lowest sequencing depth of the three samples of each soil, Table 2).
For cases when there are two adjacent binding sites apart by 60 bp as the example shown in Figure 3C, we observed that the SeqSite successfully distinguish two binding sites except for the lowest sequencing depth, although the locations tend to be closer to each other than the true sites.
The 454 system generates long sequences but suffers from low sequence depth.
The limited performance of Solexa technology as compared to 454 is likely due to the short Solexa reads and the relative low sequence depth obtained.
These values are clearly underestimates as a result of low sequence depth (1000 Genomes Project Consortium 2012).
Many of the false positive contigs probably had low coverages and read depths due to low sequence depth.
This low genome coverage made it likely to detect true genetic variation already at a low sequence depth.
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