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To increase the mapping percentages of tag sequences, two different reference databases were employed, which included G. raimondii genome and G. arboretum genome.
However, subsequently, we used two databases described in the methods to map the tag sequences, which obviously increased the mapping percentages of tag sequences.
The comparable RNA-seq read mapping percentages of the B6 and the non-B6 strains (Table 1), suggests that near-optimum alignment for each strain was achieved using the B6 reference genome; however great care must still be taken to reduce or avoid potential alignment artifacts stemming from aligning non-B6 RNA-seq reads to the B6 genome.
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The most divergent line (A1-73) had the lowest mapping percentage of any of the of the A-genome diploid accessions.
Among the 8,569,657 L. fulva reads that mapped to the I. elegans transcriptome, 4,565,885 (5.9%) mapped as singletons and 4,003,772 (5.2%) reads as pairs, generating an overall mapping percentage of 11.1%.
We assessed the quality of the assemblies based on the total number of transcripts, open reading frames predicted using Transdecoder and highest mapping percentage of the reads using GSNAP.
Amongst the climate and land use variables, MAP, percentage of agriculture and percentage of vegetation were the key determinants of AOB diversity.
- Mapped: Percentage of total reads that could be aligned to the human genome (hg18/NCBI).
We mapped the percentages of LSRs onto the species tree (Figure 2, see Table S3 for detailed retrofamily distribution).
In total, 1,669 SNP loci were detected among the 1,233 markers on the final map and percentages of different SNP types were investigated (Table 3).
For DArT, microsatellite (SSR) and gene markers mapped on each component map, the percentage of markers unique to that map (i.e. not mapped in any of the six other component maps) are given in parentheses.
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