## Description

This track shows the Zebrafish Zv8 (Dec. 2008) assembly provided by The Wellcome Trust Sanger Institute. It contains scaffolds (supercontigs) totaling 1,481,241,295 bp. The assembly has been tied to the fingerprint contig (FPC) map (data freeze December 12, 2008), which provides a tiling path of sequenced clones. 1.48 Gb of sequence from 9,816 sequenced clones (8,276 finished and 1,090 unfinished) were used as a scaffold for the assembly. Gaps were filled with contigs from a whole genome shotgun (WGS) assembly of 6.5-7x coverage comprised of reads from a library created from a single Tuebingen doubled haploid zebrafish. Approximately 1.32 Gbp (89%) of the resulting integrated assembly were placed on chromosomes 1-25, including estimated gap sizes and 100 bp gaps inserted betweeen scaffolds. The complete sequence of the mitochondrion genome, which is shown as chrM in the Genome Browser, was obtained from GenBank.

The entire assembly consists of chrM, 25 chromosomes, and 11,598 unplaced scaffolds that fall into three groups:

- Zv8_scaffold100.1 - sequences based on FPC contigs or linked to chromosomes via a marker (30,890 contigs in 180 unmapped scaffolds) where scaffold100 is the scaffold identifier, .1 represents the contig number within the scaffold. Contig numbers start at 1 and continue for each contig that is part of the same scaffold.
- Zv8_NA10001.1 - WGS contigs that could not be related to any FPC contig and could not be be placed on a chromosome (28628 contigs in 11,418 unmapped scaffolds) where NA10001 is the scaffold identifier, .1 represents the contig number within the scaffold. Contig numbers start at 1 and continue for each contig that is part of the same scaffold.
- CU862018.4_00005 - Unfinished WGS contigs parts whose exact order and orientation may not be correct (5628 unmapped contig parts). CU862018 is the contig identifier, .4 represents the version of the contig, and 00005 represents the tentative position of the contig part within the unfinished contig.

The unplaced scaffolds contain 100 bp gaps that are shown in the Gap annotation.

All components within this track are of fragment type "W" (WGS contig) except for chrM, which is type "F" (Finished).

In dense mode, this track depicts the path through the draft and finished clones (aka the golden path) used to create the assembled sequence. Clone 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 the relative order and orientation of the scaffolds between the two blocks is known, a line is drawn to bridge the blocks.

For detailed information on the methods used to produce this assembly, see the Wellcome Trust Sanger Institute Danio rerio Sequencing Project website.

## Credits

The Zv8 Zebrafish assembly was produced by The Wellcome Trust Sanger Institute, in collaboration with the Max Planck Institute for Developmental Biology, the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), and Yi Zhou, Anthony DiBiase and Leonard Zon from the Boston Children's Hospital.