Altogether, from the three BRL datasets of the infected samples, 0.24% of the non apple-derived reads (>16 nt in length) mapped onto the six ASGV genomes.
Similarly, the 5′ (15,709-bp) region of contig AAEL01000024 (36,266 bp in length) mapped to chromosome 7, the 3′ region (nucleotides 25,790-36,266) mapped to chromosome 2, while the middle region containing the rRNA unit mapped to chromosomes 1, 2, 7, and 8.
To account for small differences in unit cell length, maps were excised (fft, mapmask, maprot, and npo) and placed into the same cell before subtraction.
On the basis of the genetic map, we found eight smaller scaffolds varying from 1100 to 3400 bp in length that mapped within larger scaffolds.
Partial reads were 76 bp in length and mapped at least 30 bp to the region.
The sequence reads were of 36 or 50 bp in length and mapped to the reference murine genome assembly NCBI37/mm9 using Bowtie.
Raw read sequences, averaging 175 bps in length, were mapped with DNA databases of human, bacteria, fungi and virus genomes using the CLC Genomics Workbench bioinformatics tool.
Trimmed reads ranging between 79 bp and 82 bp in length were mapped to the complete genome sequence of lineage 2 WNV isolate SA 93/01 [GenBank: EF429198] to obtain a consensus sequence (Table 3).
To identify potential chimeric sequences, we analyzed the FASTY hits in the protein NR database and applied the following simple procedure: Matches of at least 100 bp in length were mapped back to the TC sequences to identify the regions that are covered by a match.
