Modern Human Seq Track Settings
 
Alignments of Sequence Reads from 5 Modern Humans   (All Neandertal Assembly and Analysis tracks)

Display mode:       Reset to defaults   

Display read names
Attempt to join paired end reads by name
Minimum alignment quality:

Color track by bases: Help on base coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion

Additional coloring modes:
Color by strand (blue for +, red for -)
Use gray for
No additional coloring

Display data as a density graph:

BAM configuration help

List subtracks: only selected/visible    all
  Sample↓1   Track Name↓2  
 
hide
 San  San (HGDP01029) Sequence Reads   schema 
 
hide
 Yoruba  Yoruba (HGDP00927) Sequence Reads   schema 
 
hide
 Han  Han (HGDP00778) Sequence Reads   schema 
 
hide
 Papuan  Papuan (HGDP00542) Sequence Reads   schema 
 
hide
 French  French (HGDP00521) Sequence Reads   schema 

Description

The Modern Human Seq track shows human sequence reads of five individuals mapped to the human genome. The purpose of this track is to put the divergence of the Neandertal genomes into perspective with regard to present-day humans.

Display Conventions and Configuration

The sequence reads (query sequences) from each of the five individuals are contained in separate subtracks. Use the checkboxes to select which individuals 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 is a list of the tags associated with this track. For this track, those starting with X are specific to the Burrows-Wheeler Aligner (BWA).

  • XT: Type: Unique/Repeat/N/Mate-sw
  • NM: Number of nucleotide differences (i.e. edit distance to the reference sequence)
  • SM: Mapping quality if the read is mapped as a single read rather than as a read pair
  • AM: Smaller single-end mapping quality of the two reads in a pair
  • X0: Number of best hits
  • X1: Number of suboptimal hits found by BWA
  • XM: Number of mismatches in the alignment
  • XO: Number of gap opens
  • XG: Number of gap extentions
  • MD: String for mismatching positions in the format of [0-9]+(([ACGTN]|\^[ACGTN]+)[0-9]+)*

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".
  • Attempt to join paired end reads by name: When checked (default), reads with the same name will be joined into pairs for display, with a line drawn between them.
  • 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, base qualities, or unpaired ends. 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). When "unpaired ends" is selected, items that were paired in sequencing but whose mate was not mapped are colored gray, while singletons and properly paired items are black. Alignment quality is the default.

Methods

The genomes of a San individual from Southern Africa (HGDP01029), a Yoruba individual from West Africa (HGDP00927), a Han Chinese individual (HGDP00778), an individual from Papua New Guinea (HGDP00542), and a French individual (HGDP00521) from Western Europe were sequenced to 4- to 6-fold coverage on the Illumina GAII platform. These sequences were aligned to the human reference genome (NCBI36/hg18) using the Burrows-Wheeler Aligner (BWA). Reads with an alignment quality of less than 30 were not included in these data. Those with an alignment quality greater than or equal to 30 were analyzed using a similar approach to that used for the Neandertal data.

Credits

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

References

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.

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009 Jul 15;25(14):1754-60.