## Description

This track shows the draft assembly of the $organism genome.

The Pongo pygmaeus abelii whole genome shotgun data from primary donor-derived reads (Susie, a female Sumatran orangutan housed at the Gladys Porter Zoo (Brownsville, TX)) were assembled using PCAP (Huang, 2006) with stringent parameters derived by eliminating detectable global mis-assemblies (interchromosomal cross-overs determined by alignment of the orangutan genome against the human genome) larger than 50 kb. Sequences were obtained from plasmids, fosmids, and BAC-end sequences (from CHORI-276 also obtained from "Susie"). A fingerprint map with a target of 12X clone coverage is currently in progress.

Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human with a maximum gap size allowed of 30 kb.

The assembly data were aligned against the human genome at UCSC (B. Raney) utilizing BLASTZ (Schwartz 2003) to align and score non-repetitive orangutan regions against repeat-masked human sequence. Alignment chains differentiated between orthologous and paralogous alignments (Kent 2003) and only "reciprocal best" alignments were retained in the alignment set. The orangutan AGP files were generated from these alignments in a manner similar to that already described (The Chimpanzee Genome Sequencing and Analysis Consortium 2005). Documented inversions based on primarily on FISH data (Rocchi, personal communication) as well as inversions suggested by the assembly and supported by additional mapping data (e.g. fosmid end sequences against the human assembly, (Chen and Eichler, personal communication)) were introduced as was the separation of alignments to human chromosome 2 into chimpanzee chromosomes 2A and 2B. Finally, 78 finished BAC (CHORI-273) clones were integrated into the final chromosomal sequences.

In dense mode, this track depicts the contigs that make up the currently viewed chromosome. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within a chromosome is always known; therefore, a line is drawn in the graphical display to bridge the blocks.