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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.
Figure 1 provides a summary of the alignment results and the proportion of reads carrying the HpaII sequence tag across the 17 samples.
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.
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).
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.
Thus, is the proportion of reads which have hexamer h at position i and is the proportion of reads starting with hexamer h.
Then, the proportion of reads with no errors at position i is (1 − e i ).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com