Extraction of reads from multifasta files, assignment of reads to individuals and generation of alignments of variants present in each amplicon were performed with jMHC software [ 42].
Extraction of sequences, assignment of reads to individuals and generation of alignments of variants present in each amplicon was performed with the custom software written in Java and available from http://code.google.com/p/jmhc/.com/p/jmhc/
Protein sequence alignments of variants of TuA3-460 gene with s- and m-type genes characterized previously at the Glu-B3 and Glu-D3 loci in common wheat and m-type genes in T. urartu.
From an operational perspective, BPS entails the alignment of process variants against a master process, which is also referred to as archetype, standard, or base process (Münstermann et al. 2010; Reichert et al. 2015; Tregear 2015).
After the amino acid sequence alignment of both variants, ten residues were identified that could lead to a different protein surface potential for trypsinogen.
The alignment of PA variants to a reference genome, depending on its complexity, will detect a significant number of highly similar hits distributed across different chromosomes thereby limiting the utility of PA markers for the precise mapping of associated traits or ordering sequence contigs generated in genome sequencing projects.
While it remains possible that nucleotide differences in variant 2 are the result of allelic variation, alignment of the transcript variant 2 sequence with available genomic sequences suggests that the differences in amino acids 4 56 between variants 1 and 2 may be due to sequencing errors.
The numbers of raw reads, after QC, alignment statistics, numbers of variants pre- and post-filters are provided in Additional file 2. We estimated cross-contamination using ContEst (June 2013) in the tumor samples (Additional file 16).
Using the retained variants of 201,353 after application of QUAL ≥ 30, DP10 per variant location, MQ ≥ 30, and presence of reads from two or more plants in an alignment, the number of variants showing presence of wild-type reads as well were determined.
Selecting a sample displays the alignment of all corresponding variants.
