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A SNP-index is the proportion of reads harboring the SNP that are different from the reference sequence.
At higher sequencing depth, more genes, known and novel transcripts were identified and larger proportion of reads were allowed to map across splice junctions.
The median proportion of reads with K65R was similar in the forward (0.93%) and reverse (1.2%) UDPS reads.
Consistently, there is a reduction in the proportion of sRNA reads derived from transposons and centromeric regions, whereas the proportion of reads for miRNAs and ta-siRNAs is increased 4.5-fold (Table 1).
A large proportion of read pairs could be determined in this way, the remainder were treated as unpaired reads during the assembly process.
Figure 1 provides a summary of the alignment results and the proportion of reads carrying the HpaII sequence tag across the 17 samples.
The proportion of reads was even higher (78%) if the OTUs present in a minimum of one sample of each region were considered (Table 5).
The MR fraction had the greatest proportion of reads with hits (0.67%), followed by HR (0.64%), SL (0.24%) and TS (0.18%).
In addition, a small proportion of reads could be mapped to coding sequences, which are likely to be RNA degradation products.
Protocols for paired-end sequencing at 75 bp may reduce the proportion of reads that have multiple matches in the genome and originate in low-complexity DNA regions.
For eight of the 16 repeated subtype C samples, the proportion of reads with K65R was >1.0% in each of the duplicate runs and for seven of the 16 repeated subtype C samples, the proportion of reads with K65R was <1.0% on both runs.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com