Armadillo Baboon Black Lemur Cat Chicken Chimpanzee Colobus Monkey Cow Dog Dusky Titi Elephant Galago Gibbon Gorilla Ground Squirrel Guinea Pig Hedgehog Horse Horseshoe Bat Little Brown Bat Macaque Marmoset Mouse Lemur Orangutan Owl Monkey Pig Platypus Rabbit Rat Ring-tailed Lemur Sheep Shrew Squirrel Monkey Tenrec Tetraodon Torafugu Vervet Monkey Wallaby Totals Dasypus novemcinctus Papio anubis Eulemur macaco macaco Felis catus Gallus gallus Pan troglodytes Colobus guereza Bos taurus Canis familiaris Callicebus moloch Loxodonta africana Otolemur garnettii Nomascus leucogenys leucogenys Gorilla gorilla gorilla Spermophilus tridecemlineatus Cavia porcellus Atelerix albiventris Equus caballus Rhinolophus ferrumequinum Myotis lucifugus Macaca mulatta Callithrix jacchus Microcebus murinus Pongo pygmaeus Aotus nancymaae Sus scrofa Ornithorhynchus anatinus Oryctolagus cuniculus Rattus norvegicus Lemur catta Ovis aries Sorex araneus Saimiri boliviensis boliviensis Echinops telfairi Tetraodon nigroviridis Takifugu rubripes Chlorocebus aethiops Macropus eugenii Total BACs 25 15 8 20 7 13 14 15 9 17 24 13 16 11 16 15 25 14 16 15 14 13 10 13 18 10 16 17 17 10 15 19 15 12 3 2 13 16 541 Total Mb 2.63 2.26 1.41 2.11 0.84 1.73 2.12 2.34 1.34 2.29 2.25 2.17 2.43 1.94 1.91 2.01 2.86 2.13 1.98 2.16 1.79 2.13 1.76 2.02 2.39 1.50 1.68 2.32 2.16 1.51 2.18 2.07 2.38 1.92 0.32 0.17 1.93 2.05 73.20 Total BACs 137 110 105 78 88 138 99 83 89 93 130 95 97 60 88 76 95 115 73 95 87 2,031 Total Mb 18.8 19.2 14.6 16.2 15.3 18.8 18.5 14.9 13.4 15.6 19.4 15.5 19.0 13.8 15.3 10.8 17.4 15.7 14.6 17.1 14.5 338.5 Blakesley et al. BMC Genomics 2010, 11:21 http://www.biomedcentral.com/1471-2164/11/21 Page 3 of 15 Table 1 Human-grade finished BAC sequences from ENm001. Table 2 Comparative-grade finished BAC sequences listed by species. Common name Taxonic name The total number of BACs (Total BACs) and the amount of non-redundant human-grade finished sequence generated (Total Mb) for each species within genomic region ENm001 are shown. Mb of individual BAC clone sequences) for ENr231, EN232, and ENr333 were 64 (10.3 Mb), 51 (8.0 Mb), and 62 (10.0 Mb), respectively. Misassembled sequence In shotgun sequencing, once a sufficient number of sequence reads are collected based on the size of the starting template (e.g., a BAC), the sequence is assembled computationally (such as with the program Species Armadillo Baboon Cat Colobus Monkey Dusky Titi Elephant Galago Gibbon Ground Squirrel Guinea Pig Hedgehog Horseshoe Bat Marmoset Mouse Lemur Owl Monkey Platypus Rabbit Shrew Squirrel Monkey Tenrec Vervet Monkey Totals The total number of BACs (Total BACs) and the amount of comparative-grade finished sequence generated (Total Mb) for each species are shown. Phrap [25,26]). Even though the assembly program is operated under conditions we have optimized for our BAC sequences, occasionally an incorrect alignment occurs with closely related but distinct reads, resulting in a misassembled and incorrect consensus sequence. Misassemblies can result from various causes, such as the presence of multiple copies of closely-related repeti- tive sequences that inappropriately collapse onto one or a few regions. Often, misassemblies incorrectly portray non-adjacent segments as being contiguous. Such pro- blems require manual correction, otherwise the sequence would be of marginal utility (e.g., for accu- rately identifying genes or characterizing the long-range organization of a genomic region). With the aid of sequence-editing programs, an experienced technician systematically reviews and sorts the misassembled reads, eventually correcting problems and allowing a valid con- sensus sequence to emerge. However, this manual inter- vention can be one of the most labor-intensive and costly components of the sequence-finishing process. Details of our sequence-finishing process are provided in the Supplementary Materials associated with Blakes- ley et al. [5]. We have consistently found that certain genomic regions are more prone to sequence misassemblies than others, regardless of the species being studied. For