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. 2005 Aug;15(8):1023–1033. doi: 10.1101/gr.3771305

Table 2.

Polymorphisms detected in the assembled B. pennsylvanicus genome

Polymorphisms 497
    Indels 52
        Average size, bp 1.58
        Intergenic regions 50
        Pseudogenes 0
        RNAs 0
        ORFs 2
    SNPs 445
        Transitions 331
        Transversions 114
            Ratio 2.9
        Intergenic Spacers 156
        Pseudogenes 5
        RNAs 1
        ORFs 283
            Synonymous 176
            1st 7
            2nd 1
            3rd 168
            Nonsynonymous 107
            1st 66
            2nd 37
            3rd 4

Nucleotide polymorphisms were recorded for all sites in the genome where high quality (>40 PHRED score) disagreements occurred, and where both variants were represented by multiple clones (at least two clones, and typically many more). The two indels within ORFs did not disrupt the reading frame, but rather resulted in amino acid insertions or deletions, that is, insertion/deletion of a leucine and lysine in sucA (sites 348-349 of the protein sequence) and the insertion/deletion of an alanine in aroE (between sites 126 and 127 of the protein sequence).