Data for the Saqqaq genome project – Bioinformatics Centre - University of Copenhagen

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Bioinformatics Centre > Saqqaq

Data for the Saqqaq genome project

This page holds links to sequence data for the sequencing of a 4000 year old human genome described in

Rasmussen et al, Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo , Nature 463, 757-762 (11 February 2010)

Browsing the genotyping data 

Feb 24, 2010: The data are now available in our mirror of the UCSC genome browser in the Human, Mar 2006 assembly. The track is called "Saqqaq SNPs" and is found in the "Variation and Repeats" section. You can press this link to go directly to an open track.

Genotyping data

There are two data sets described in the online supplementary material: The complete genotyping data and the high-confidence data. The data format is described below.

Data format

The two data sets contain data in the same format.

Files with the extension ".diff" holds positions that are different from the reference human genome (hg18 ). Files with the extension ".same" holds positions that are the same as the reference human genome (compressed with gzip).

The files all have the same format and contain the genotype for each position (always relative to the hg18 plus-strand) and information about posterior probability etc. The files have the following tab-separated columns:

  1. The chromosome name
  2. Position using 0-indexation (*)
  3. The reference nucleotide in hg18
  4. Indicates whether the genotype is the same as the reference nucleotide (y) or not (n)
  5. Genotype called by the program SNPest (see supplementary material)
  6. (1-PP), where PP is the posterior probability of the genotype.
  7. Depth. The number of reads covering the position
  8. Repeat: If the position lies in an annotated repeat, the ID is given here (otherwise it is '-')
  9. Distance to nearest SNP (always 1 in the .same-files)
  10. RS-number: If the position overlaps an annotated SNP, the dbSNP rs-number is given (otherwise it is '-', and in that case the next three fields are also '-')
  11. Type of dbSNP entry ('single', 'indel' etc. - see the UCSC genome browser for details).
  12. Strand for dbSNP entry ('+' or '-')
  13. Type of SNP (e.g. 'AC' for a SNP of type 'single')

* Note that chromosomal positions start at 0. In the UCSC Genome Browser and many other ressources, counting starts at 1, so add one to the numbers in the above mentioned files to compare to these ressources.

Contact Stinus Lindgreen if you have questions regarding the data or the format.