Exact(6)
Read size, quality values, N positions, base composition were calculated and known adapters sequences were detected before and after filtering the reads.
SNP positions (base pair [bp]) and function were identified using the SNPper (http://snpper.chip.org) database NCBI Build 35.1 (Table 1).
Gene names, marker positions (base pair – bp) and marker function were identified using the SNPper database (http://snpper.chip.org).
Marker positions (base pair - bp), marker function, and amino acid changes were identified using the SNPper (http://snpper.chip.org) database and using NCBI Build 35.1.
More than 35,873 different carbohydrate sequences have been uploaded in GlycoCT format with 11,822 structures fully determined including all linkage positions, base type, anomers, ring size and modifications [ 82, 83].
The resulting 76-bp paired-end reads were assessed for quality using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc, last accessed November 2, 2011) and filtered with FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html, last accessed August 5, 2011) to exclude reads where less than 90% of positions base calls had quality scores of Q20 or above.
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