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Chromosome Summary

A zoomed-in view of a chromosome including graphical displays of known and novel genes, percent of GC repeats, and SNP density. Click on the chromosome to zoom in to 'Region in Detail', in order to view positions of genes and other annotation. Add your own annotation to one chromosome, or a karyotype, using the control panel and this view, or the 'Karyotype' view.

Each species in Ensembl has a number of statistics for sequence length. These statistics are also found on species-specific 'home pages' and are calculated as follows. Some counts are only available from the species home page.

Base Pairs per chromosome
These are pre-calculated in order to speed up page display, and stored in the seq_region table of the core database. The number is based on the assembled end position of the last 'seq_region' in each chromosome (from the AGP file), or if there is a terminal gap it is set to the assembled end location of that terminal gap.
For the haplotype chromosomes (c6_COX etc), although there is only haplotype-specific sequence for a small region of the chromosome, the length of the seq_region is set to the full length of the chromosome including the specific haplotype (eg. c6_COX is 170899992bp long).
Gene summaries
The number of gene types are listed below the chromosome, and are as follows:
  • Known Gene Count gives the number of 'known' genes that Ensembl has predicted on this chromosome. 'Known' genes have been mapped by Ensembl to near-full-length species-specific protein sequences already available in the public sequence databases.

  • Novel Gene Count the number of 'novel' genes that Ensembl has predicted on this chromosome. 'Novel' genes, although predicted on the basis of similarity to protein or cDNA sequences and/or ESTs, could not be mapped with confidence to existing entries.

  • Pseudogenes and non-coding (nc)RNA genes Ensembl annotates several sub-classes of ncRNA genes. Counts per RNA gene class are available from this page.

  • Please note: Gene counts presented per chromosome on Ensembl 'Chromosome' views are for only the areas shown. Gene counts for all chromosomes may not add up to the numbers presented for the whole genome on the species-specific home pages. This is due to extra-chromosomal sequences, which are annotated with genes but not necessarily displayed. The count differences are also due to the fact that pseudo-autosomal regions (PAR) on the human X and Y chromosomes count towards the whole-genome statistics only once.

  • SNP Count lists the number of SNPs that Ensembl has placed on this chromosome.

  • (Species Home Page) Base Pairs (whole assembly)
    The total number of base pairs for the entire assembly is the sum of all sequences in the dna table of the core database. It is available from the species-specific home page. This includes redundant regions such as haplotypic sequences and the pseudo-autosomal region (PAR) of the Y chromosome in human, and gaps in Drosophila melanogaster. See the assembly details of each species for more information.
    (Species Home Page) Golden Path
    The "golden path" is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs.