## Description

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.

## Display Conventions and Configuration

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:

- AS: Alignment score generated by aligner

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.

- Display Read Names: By default, read names are not displayed. To display the read names, selected the check box next to "Display read names".
- Minimum alignment quality: Excludes alignments with quality less than the given number. The default is 0.
- Color track by bases: By default, mismatching bases are highlighted in the display. Change the selection to "item bases" to see all base values from the query sequence, or "OFF" to ignore query sequence. Click here for additional information.
- Alignment Gap/Insertion Display Options: Click here for help with these options.
- Additional coloring modes: Other aspects of the alignments can be displayed in color or grayscale.

- Color by strand: Alignments on the reverse strand are colored dark red, alignments on the forward strand are colored dark blue.
- Grayscale: Items are shaded according to the chosen method: alignment quality or base qualities. The alignment qualities of individual items are shaded on a scale of 0 (lightest) to 99 (darkest). Base qualities are shaded on a scale of 0 (lightest) to 40 (darkest). Alignment quality is the default.

## Methods

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.

## Credits

This track was produced at UCSC using data generated by Ed Green.

## References

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.