Schema for Neandertal Mito - Neandertal Mitochondrial Sequence (Vi33.16, 2008)
  Database: hg19    Primary Table: ntMito    Row Count: 1   Data last updated: 2010-12-15
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 16361int(10) unsigned range Number of bases that match that aren't repeats
misMatches 194int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 2int(10) unsigned range Number of inserts in query
qBaseInsert 10int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 16int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NC_011137.1varchar(255) values Query sequence name
qSize 16565int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 16565int(10) unsigned range Alignment end position in query
tName chrMvarchar(255) values Target sequence name
tSize 16571int(10) unsigned range Target sequence size
tStart 0int(10) unsigned range Alignment start position in target
tEnd 16571int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 309,204,15660,76,306,longblob   Size of each block
qStarts 0,310,514,16174,16259,longblob   Start of each block in query.
tStarts 0,312,520,16181,16265,longblob   Start of each block in target.

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851636119400210416+NC_011137.116565016565chrM165710165715309,204,15660,76,306,0,310,514,16174,16259,0,312,520,16181,16265,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Neandertal Mito (ntMito) Track Description
 

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.