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In order to have a balanced representation of the 4 amplicons, we calculated the average coverage at the level of the amplicons (and not of the entire region) and joined the amplicons with the same average coverage, considering them as a single (artificial) sampling event.
Instead, we consider a relative measure of nucleotide diversity β t developed by Novaes et al. [ 12], defined for contigs with average coverage at least 2×.
Indeed, focusing only on average coverage at global or country levels may hide variability among countries and within countries among districts.
We next assessed potential biases in transcript representation (i.e. coverage at 3′ and 5′ end) by determining the average coverage at each percentile of length from 3′ to 5′ end of the known transcripts.
In our study, the average coverage at this valley always remains below 0.23 in all groups (reaching as low as 0.09 in the CON group), except the SIL group where it is above 0.35.
A single fixed cell had an average coverage at 20× depth of 30% when sequencing to an average of 40× depth, whereas a single unfixed cell had 45% coverage.
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In this study, we used whole-genome sequence data derived from 2230 Icelanders sequenced to an average coverage of at least 10× using Illumina GAIIx and HiSeq2000 instruments at the deCODE Genetics facility.
This provided approximately 26.89x average coverage depth at the completion of this funding phase.
The average coverage was at a minimum of 59.65× and a maximum of 141.56× per genome.
Variants were identified by whole-genome sequencing of 2230 Icelanders to an average coverage of at least 10×.
Mean non-N reference coverage (after excluding gaps) is ~36X with 95.5% of the positions having an average coverage of at least 10X.
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