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The average mapping rate was 77.7%.
An average mapping rate of ~83% (164.66 million mapped reads) was reached.
The average mapping rate across libraries was 86 %, the value for each library ranging between 60 % and 92 %.
Reads were then mapped to the Ae.aegypti genome sequence (Aaeg L1.2 gene set, http://vectorbase.org) using the Tophat algorithm with default parameters (http://tophat.cbcb.umd.edu, release 1.0.14) [ 67], leading to an average mapping rate of 80%.
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In the "transcriptome + genome" mapping mode, the average mapping rates for Ensembl, RefGene, and UCSC increased to 96.7%, 94.5%, and 94.6%, respectively, and the mapping rate difference among different gene models decreased.
Approximately 85%% of the reads in each library were uniquely mapped to the galGal4 assembly of the chicken genome, and the average mapping rates were 83.0 and 84.2 % for the L20 and L30 groups, respectively (Table 1).
The average coverage across all samples was 507, whereas the mean mapping rate reached 94%.
Mapping quality was assessed using RSeQC and RNA-SeQC [ 33, 34], which indicated an average read mapping rate of 95.4%% (Additional file 2c), with 92.7 % of reads mapped to intragenic sequences (Additional file 2d) and an average coverage per base of 9.84 reads (Additional file 2e).
The average read mapping rates were 86%, 69%, and 70% for Ensembl, RefGene, and UCSC annotations, respectively.
Therefore, some farms may have higher ELISA values than average because they have higher than average MAP infection rates or because they have some cows producing high concentrations of MAP antibodies.
When aligned with IRGSP-1.0 using the BWA software, the average genome coverage and mapping rate were 94.0% and 92.5%, respectively.
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CEO of Professional Science Editing for Scientists @ prosciediting.com