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For this purpose, we extracted all fish sequences alignable to a human region according to the fish-human pairwise alignments downloaded from the UCSC Genome Browser.
Consistent with this, only a small proportion of the plasmid was alignable to our 36-nucleotide Illumina sequence reads.
In total, we analyzed 1168 regions, which represented 1.26 Mbp of sequence alignable to chimp and rhesus genomes.
In total, respectively, 2.1 Mbase, 7.6 Mbase, and 7.5 Mbase of sequence alignable to chimp and rhesus genomes have been studied (supplementary table 2, Supplementary Material online).
Third, sequences corresponding to the location of the anchor reads were downloaded from UCSC genome browser website, candidate micSeqs that are alignable to those sequences are removed.
Mappability is a measure of the uniqueness of a given genomic sequence based on the number of sequenced fragments uniquely alignable to that sequence.
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Yet this may include probes that match unannotated transcripts, or transcripts which are non-alignable to the current genome.
No assembly produced a contig or scaffold that was un-alignable to the reference genome, and all had identities that were over 99.9% (Table 6).
Certain insertions were manually removed after sequence alignments to maximize alignable regions prior to calculating the polymorphism parameters.
The contigs were first aligned to GRCh37, human NCBI RefSeq genes and human EST sequences to remove the alignable contigs with the threshold of 90% identity and 90% coverage.
The availability of sequence-tagged markers such as RFLP probes and SSR in the Cotton Marker Database (http://www.cottonmarker.org/) and a cotton consensus map (Rong et al. 2005a) provides alignable information to convert genetic positions (in centiMorgans, cM) of markers to physical positions (bp).
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