A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

Kerrin S Small¹ , Michael Brudno² , Matthew M Hill¹ and Arend Sidow¹

¹Departments of Pathology and of Genetics, Stanford University Medical Center, 300 Pasteur Drive, Stanford, California 94305-5324, USA

²Department of Computer Science, Banting and Best Department of Medical Research, University of Toronto, Toronto, 6 King's College Rd, Ontario, M5S 3G4, Canada

author email corresponding author email

Genome Biology 2007, 8:R41doi:10.1186/gb-2007-8-3-r41


Published:	20 March 2007

Subject areas: Genome studies, Model organisms, Bioinformatics, Evolution

Additional files

Additional data file 1:

In this figure supercontigs are black lines denoted with purple letters. Regions of long alignment are denoted in turquoise (approximately to scale), with the length of the alignment in megabases. Regions of short alignment are denoted in pink (grossly out of scale to make them visible), with the length of the alignment in kilobases. Approximate positions of genetic markers are given by orange ovals, and their names are in blue. Linkage is shown by a red dashed line with the genetic distance indicated. Lack of a red dashed line between any two markers indicates no detectable linkage. Positions where the assembly is broken to account for the genetic map data are shown as circled lightning.

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Additional data file 2:

In this figure the x-axis diplays the maximum read coverage per contig and the y-axis displays the percentage of contigs in a category. Red bars indicate unassigned contigs, and blue bars indicate contigs assigned to an allelic bin.

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Additional data file 3:

A figure displaying the length distribution of predicted contig overlaps in the original WGS assembly.

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