Physical Map of the Sugar Beet Genome

Help   FAQ   Download
Search examples:
z25F6, 045E07, BQ595006, HN147957

Chromosome 1
Chromosome 2
Chromosome 3
Chromosome 4
Chromosome 5
Chromosome 6
Chromosome 7
Chromosome 8
Chromosome 9

Table Content

For each chromosome an overview table is provided showing the list of genetic markers and their integration into the physical map with links to the physical contigs.

Column: Clone or probe

Clone and probe names as used in the physical map contigs. Clone names begin with "z" or "s" referring to the clone libraries ZR or SBI, respectively. The list of genetic markers contains "z"-clones only because clone markers were generated only from the ZR library. The clone names are linked with the GenBank entry for their corresponding BAC end sequences (sometimes only one end is available). Probe names have the format "plate (3 digits), row (1 digit), column (2 digits)". Some probes have custom names (eg. eP-A07 or einz11). All probes are linked with their 35mer oligo sequence in fasta-format appearing at the very top of the page. GenBank accessions for the source sequences are indicated in the description lines.

Column: Source Seq

For clones: GenBank link to the BAC end sequence where a genetic marker was derived from. For probes: GenBank link to the source sequence where the oligomer was designed from and a genetic marker was derived from.

Column: Marker

Names of the markers in the genetic map. The link points to the polymorphic sequence used for the marker assay.

Column: Chr

The chromosome where markes were genetically mapped and physical contigs were anchored.

Column: cM

The centi-Morgan position where markes were genetically mapped. These positions were used as anchor points for physical contigs. In some cases the markes have a different order within physical contigs than suggested by the cM position. The table was sorted according to the order of markers within physical contigs.

Column: Contig pdf

Physical contig showing the order of probes (columns) and clones (rows, names alternating on either side) as determined by the analysis of hybridization results. Filled rectangles indicate a positive hybridization result for the probe in this column with the clone in that row. Colors refer to the chromosomes of chromosomally localized probes or clones: orange - chr1, grey - chr2, yellow - chr3, red - chr4, light blue - chr5, green - chr6, pink - chr7, dark blue - chr8, purple - chr9.

Column: Contig html

Similar to 'Contig pdf' but containing html links for probe names and clone names. All probes are linked with their 35mer oligo sequence. The target file in fasta format contains the GenBank / NCBI accession number(s) for the source sequences of the oligomer. For some clones BAC end sequences are available. Those clones are linked with their NCBI entry.

Design from (adapted).