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Since read numbers per sample varied, to avoid bias we used copy number of relative reads depth (CNR), which was defined as total counts divided by the median read number, to represent the CNVs for each sample.
The median read number per CDS was above 1,000 (log value >3).
The range of reads mapped to a gene was comparable across runs, with the 9 lanes of increased sequence counts displaying a slight increase in median read number per gene.
For all the 6 transcriptomes obtained by RNAseq (2 isolates and 3 treatments), the median read number per COG class was calculated to distinguish the most represented classes at the quantitative level in the transcriptomes.
The lower median read number per CDS obtained from the RNAseq data of STM 4661 can be attributed to the larger number of reads mapped on ribosomal RNAs as well as the higher CDS number that was predicted in this isolate.
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Median contig length and the mean read number per contig were 226 bp and 25.5, respectively.
The mean read number was 3.2x104.
EST read number ranged from 2 reads to 3,161 reads in a contig, with a median of 23 EST reads per contigs.
jMHC removed the imperfect sequences reducing the read number to 439,284 (68.8% of the previous step) with a mean of 286 reads per individual and a median of 252.
Every single day read number two above.
These numbers translate to median read counts of ~25 reads per gene per million mapped reads.
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