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Set-Cookie: hguid=2431716445_ZKitj1iEwzbESFWnZPCdrZCwRQeZ; path=/; domain=.ucsc.edu; expires=Thu, 31-Dec-2037 23:59:59 GMT Content-Type:text/html Neandertal Mito Track Settings
Neandertal Mito Track Settings
 
Neandertal Mitochondrial Sequence (Vi33.16, 2008)   (All Neandertal Assembly and Analysis tracks)

Display mode:      Duplicate track

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


Display data as a density graph:

Display data as a rearrangement graph:
Data schema/format description and download
Assembly: Human Feb. 2009 (GRCh37/hg19)
Data coordinates converted via liftOver from: Mar. 2006 (NCBI36/hg18)
Data last updated at UCSC: 2010-12-15

Note: lifted from hg18

Description

This track shows the alignment of a complete Neandertal mitochondrial sequence to a modern human mitochondrial sequence.

Note: the mitochondrion used as the genome browser reference sequence "chrM" in hg18 and hg19 is NC_001807, which has been deprecated. Future human genome browsers will use the revised Cambridge Reference Sequence (rCRS) NC_012920.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. Mismatching bases are highlighted as described here. Several types of alignment gap may also be colored; for more information, click here.

Methods

DNA was extracted from a 38,000-year-old bone and sequenced using methods described in Green, et al. The Neandertal mitochondrial sequence (NC_011137) was downloaded from GenBank and aligned to chrM (NC_001807) using BLAT.

Reference

Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell. 2008 Aug 8;134(3):416-26.