The Neandertal Seq track shows Neandertal sequence reads mapped to the $organism genome. The Neandertal sequence was generated from six Neandertal fossils found in Croatia, Germany, Spain and Russia.
The sequence reads (query sequences) from each of the six samples are contained in separate subtracks. Use the checkboxes to select which samples will be displayed in the browser. Click and drag the sample name to reorder the subtracks. The order in which the subtracks appear in the subtrack list will be the order in which they display in the browser.
The query sequences in the SAM/BAM alignment representation are normalized to the + strand of the reference genome (see the SAM Format Specification for more information on the SAM/BAM file format). If a query sequence was originally the reverse of what has been stored and aligned, it will have the following flag:
(0x10) Read is on '-' strand.
BAM/SAM alignment representations also have tags. Some tags are predefined and others (those beginning with X, Y or Z) are defined by the aligner or data submitter. The following tag is associated with this track:
The item labels and display colors of features within this track can be configured through the controls at the top of the track description page.
The Neandertal sequence was genereated from six Neandertal fossils. Vi33.16 (54.1% genome coverage), Vi33.25 (46.6%) and Vi33.26 (45.2%) were discovered in the Vindija cave in Croatia. Feld1 (0.1%) is from the Neandertal type specimen from the Neander Valley in Germany, Sid1253 (0.1%) is from El Sidron cave in Asturias, Spain, and Mez1 (2%) is from Mezmaiskaya in the Altai Mountains, Russia.
To increase the fraction of endogenous Neandertal DNA in the sequencing libraries, restriction enzymes were used to deplete libraries of microbial DNA. This was done by identifying Neandertal sequencing reads whose best alignment was to a primate sequence, and selecting enzymes that would differentially cut non-primate fragments. These enzymes all contained CpG dinucleotides in their recognition sequences, reflecting the particularly low abundance of this dinucleotide in mammalian DNA. Sequencing was carried out on the 454 FLX and Titanium platforms and the Illumina GA. Neandertal reads were mapped to the $organism genome ($db) using a custom mapper called ANFO. This custom alignment program was developed to take into account the characteristics of ancient DNA. Following the observation and implementation by Briggs et al., ANFO uses different substitution matrices for DNA thought to be double-stranded versus single-stranded and changes between them if doing so affords a better score.
This track was produced at UCSC using data generated by Ed Green.
Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science. 2009 Jul 17;325(5938):318-21.
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A Draft Sequence of the Neandertal Genome. Science. 2010 7 May;328(5979):710-22.