Because this alignment is so highly conserved at almost every position, the consensus sequence for each BHIC defaults to the reference genome used in our alignment.
The munged reads were aligned by Maq, with default parameters, to the reference sequence for each marker and the genotype called, based on counts of the bases read at the SNP position, but only if the SNP position was covered by at least 20 high quality reads (otherwise the allele is defined as unclassified, U) using Perl script BAT_SNPs.pl (Additional file 8).
Genome assembly utilized a mapping/denovo hybrid approach consisting of the following; Reads were first mapped using BWA [ 13] and default parameters to the reference FPR3757 core genome its three plasmids and the pHOU300 plasmid.
Next, each HMM is searched via hmmsearch [ 28] against a reference database (NCBI RefSeq by default) to identify reference homologs, and against all user-selected metagenomes to identify metagenomic homologs.
The complete genome of S. typhi CT18 was chosen as the reference genome, and all of the query genomic sequences were divided into possible sequences of 50 bp (default) and subsequently mapped to the reference genome via Bowtie2 with a default k-mer length of 22, allowing for one mismatch within the k-mers to maximise sensitivity.
The partner may report the borrower's default to a credit reference bureau, if there is one.
Still, the inferred TOCD&S is one of many ways to represent data and might be the favored default to serve as reference against which LGTs are displayed.
Hits were then blasted against the NCBI database [ 55] with default settings, and aligned to the reference protein sequences using the tool at the Genestream Bioinformatics Resource server [ 74].
We were originally concerned that a switching in samples was the cause of the discrepancy, but repeated genotyping and re-examination of the Sequenome iPLEX versus the sequencing data suggested that when sequence coverage was relatively low, our GATK pipeline defaulted to the genotype of the provided reference genome resulting in erroneous SNPs calls across isolates in the same time course.
Although our initial analysis used best practices at the time of original data collection, in some regions of lower sequencing coverage our GATK pipeline defaulted to the genotype of the provided reference genome, resulting in erroneous SNP calls when comparing between strains.
The borrowing rate of the investor accounts both for her credit quality and for feedback effects generated by default of the reference entity.
