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Newer sequencing technologies generate longer reads, which will allow more read pairs to be aligned uniquely to this highly repetitive region, resulting in higher coverage and more power to detect variants.

Since about 86% of reads sampled in silico from PstI or BsrFI restriction sites could be aligned uniquely to the genome, it appears that 13%to29%9% of sites were not sampled by RAD library preparation.

Sequencing reads could be aligned uniquely to the Pcmsp1 sequence of each laboratory clone, and were used to quantify the relative frequency of each clone in the artificial mixtures.

In the case of paired end reads, if one of the members of the pair can be aligned uniquely to a certain position, the corresponding mate can sometimes be rescued if it is a multi-map.

Although short tags are most informative if they can be aligned uniquely to a reference genome, repetitive elements are not randomly distributed throughout the genome (Campbell et al., 2008); therefore, the proportion and location of uniquely mappable short sequences will also be non-randomly distributed.

The ratio of reads, Puq that are aligned uniquely to RefBAC when aligning to RefBAC + RefEX to those that are aligned to RefBAC without RefEX.

The ratio of reads, P uq that are aligned uniquely to RefBAC when aligning to RefBAC + RefEX to those that are aligned to RefBAC without RefEX.

We estimated the bisulfite conversion rate using reads that were aligned uniquely to the lambda phage genome.

Among the 217 large GI1 contigs, 61 were aligned uniquely to the optical map (Table S3, Additional file 3).

Illumina reads were aligned uniquely to the reference using bowtie (Langmead et al. 2009) with settings tolerating three mismatches in aligned reads (parameter settings: −v 3 –k 1).

Simulated reads were aligned uniquely to human chromosome 19 and reads mapping to multiple locations were output to a separate FASTA file.