Supplementary Data for

Jones, T., Federspiel, N.A., Chibana, H., Dungan, J., Kalman, S., Magee, B.B., Newport, G., Thorstenson, Y.R., Agabian, N., Magee, P.T., Davis, R.W. and S. Scherer. (2004) The Diploid Genome of Candida albicans. PNAS 101:7329-7334

Genome sequence

Supercontigs

• Supercontig naming conventions
• All supercontigs: sequence and base qualities (FASTA format)
• Reference haploid set of supercontigs: sequence and base qualities (FASTA format)
• Supercontig maps: description and maps in zip format or gzipped tar format

ORFs

• ORF selection and naming conventions
• Diploid ORF set (14217 ORFs): sequence and base qualities
• Reference haploid ORF set (7677 orfs): sequence and base qualities
• Reduced ORF set (6419 orfs): sequence and base qualities
• Cross-species blast results and table format description

Sequence not participating in the diploid assembly

• General notes
• rDNA sequence and feature table
• mtDNA sequence and feature table
• Scrap file, part 1: excluded phrap contigs. Sequence, base qualities, and notes
• Scrap file, part 2: trimmed scraps. Sequence and base qualities

Heterozygous polymorphism

• Description of polymorphism table formats
• Table of all polymorphisms
• Table of polymorphisms in ORFs
• Tables of ORF allele pairs and ORF allele status
• ORF polymorphism status table
• Table of tandem repeat locations and polymorphisms

Phrap assembly

• Phrap assembly raw contigs: sequence, base qualities, and notes