This track shows the draft assembly of the $organism genome.
In dense mode, this track depicts the path through the contigs (aka the golden path) used to create the assembled sequence. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist in the path, spaces are shown between the gold and brown blocks. If a gap between two blocks (contigs) is covered by a read pair, then a line is drawn to bridge the blocks.
The Release 1.0 D. simulans assembly, produced by the Genome Sequencing Center at the Washington University (WUSTL) School of Medicine in St. Louis, represents a mosaic of several different D. simulans lines. The assembly process began with an ~4X Whole Genome Shotgun assembly of the the D. simulans w501 line. The w501 contigs were initially anchored, ordered and oriented by alignment with the D. melanogaster genome. The assembly was then examined for places where the w501 assembly suggested inversions with respect to the melanogaster assembly. One major inversion was found, confirming the already documented inversion found by Lemeunier and Ashburner (1976). Six other D. simulans lines (c167.4, md106ts, md199s, nc48s, sim4, and sim6) were assembled with ~1X coverage. Using the 4X WGS assembly of the simulans w501 genome as a scaffold, contigs and unplaced reads from the 1X assemblies of the other individual D. simulans lines were used to cover gaps in the w501 assembly where possible. Thus the resulting assembly is a mosaic containing the w501 contigs as the primary scaffolding with contigs and unplaced reads from the other lines filling gaps in the w501 assembly.
All components within this track are of fragment type "W": Whole Genome Shotgun contig.