bde35bf9d06a82fa4d60fcf3259f43259a93b0c5
ccpowell
  Tue Jul 9 16:11:04 2019 -0700
Swapping MySQL to MariaDB in docs, refs #23597

diff --git src/hg/htdocs/Neandertal/index.html src/hg/htdocs/Neandertal/index.html
index 95b0e7b..79a9a92 100755
--- src/hg/htdocs/Neandertal/index.html
+++ src/hg/htdocs/Neandertal/index.html
@@ -1,682 +1,682 @@
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 			      <TD><A NAME="About"></A><FONT size="4"><B>&nbsp; Neandertal Genome Analysis Consortium Tracks at UCSC</B></FONT> 
 			  </TD></TR></TBODY>
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 <!-- Display image in righthand corner -->
 <TABLE ALIGN=RIGHT BORDER=0 WIDTH=250>
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       <IMG SRC="Neandertal_reconstruction.jpg" HEIGHT=251 WIDTH=167 ALT="Artist's rendering of Neandertal">
   </TD></TR>
   <TR><TD ALIGN=RIGHT> 
       <FONT SIZE=-1>Artist's rendering of Neandertal man, from <BR> Neandertal museum in Mettmann, Germany<BR> 
       </FONT>
       <FONT SIZE=-2>Copyright: Johannes Krause, 
 	<A HREF="http://www.eva.mpg.de/neandertal/" 
 	TARGET=_BLANK>Max Planck Institute <BR>for Evolutionary 
 	Anthropology</A>.  All rights reserved.
       <P>&nbsp;</P>
       </FONT>
   </TD></TR>
 </TABLE>
 
 <P>
 Neandertals are the closest extinct relatives of humans. They lived from
 several hundred thousand years ago until their disappearance approximately
 30,000 years ago. The Neandertal genome sequence 
 (published by Green <em>et al.</em> in <A HREF="http://www.sciencemag.org/special/neandertal/" 
 TARGET=_BLANK><em>Science</em></A> May 2010) consists of short
 sequence fragments, usually about 50 base pairs long, mapped to the
 human reference genome. The DNA was extracted largely from three
 Neandertal bones, each about 40,000 years old, from the Vindija Cave
 in Croatia: Vi33.16, Vi33.25, and Vi33.26. The bulk sequencing was
 carried out on the Illumina GAII platform. Neandertal DNA was
 identified from among the background of microbial sequences in the
 bone by similarity to the human or chimpanzee genomes.</P>
 <P>
 This portal provides access to the sequence data and alignments to the
 reference human genome (NCBI 
 Build 36/<A HREF="../cgi-bin/hgGateway?db=hg18">hg18</A>,
 GRCh37/<A HREF="../cgi-bin/hgGateway?db=hg19">hg19</A>) as well as the reference
 chimpanzee genome (CGSC 2.1/<A HREF="../cgi-bin/hgGateway?db=panTro2">panTro2</A>) and several associated analyses
 (see <A HREF="#Downloads">Downloads</A> and <A HREF="#References">References</A>). 
 </P>
 <P>
 The following annotations are available on the human hg18 and hg19 genome assemblies,
 except as noted:
 <UL>
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr10&position=chr10:69713986-69714099&g=ntHumChimpCodingDiff">Neandertal 
 Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage</A>: 
 Displays Neandertal alleles for human-chimp protein-coding differences 
 on the human lineage using orangutan as the outgroup to determine which allele 
 is more likely to be ancestral.
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr2&position=chr2:43309001-43314000&g=ntSssZScorePMVar">Selective 
 Sweep Scan (S) on Neandertal vs. Human Polymorphisms</A>: 
 Shows the S score, an estimate of positive selection in 
 humans within a 100 kb window surrounding each polymorphic position in the 
 five modern human sequences and the human reference genome.
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr2&position=chr2:43309001-43314000&g=ntSssTop5p">Selective 
 Sweep Scan (S): 5% Smallest S scores</A>: Shows regions of the human 
 genome with a strong signal for depletion of Neandertal-derived alleles (regions
 from the Sel Swp Scan (S) track with S scores in the lowest 5%), which may 
 indicate an episode of positive selection in early humans. 
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr2&position=chr2:43309001-43314000&g=ntSssSnps">SNPS 
 Used for Selective Sweep Scan (S)</A>: Shows single nucleotide polymorphisms 
 (SNPs) on which the S score (above) was calculated.
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr10&position=chr10:69713986-69714099&g=ntOoaHaplo">Candidate 
 Regions for Gene Flow from Neandertal to Non-African Modern Humans</A>: 
 Shows 13 regions of the human genome in which there is considerably more 
 haplotype diversity among non-African genomes than within African genomes.
 10 of these regions provide evidence for gene flow from Neandertals to 
 modern humans outside of Africa.
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr10&position=chr10:69713986-69714099&g=ntSeqContigs">Neandertal 
 Sequence Contigs Generated by Genotype Caller</A>: Shows consensus 
 contigs called from overlapping, non-redundant reads that passed mapping and 
 base quality criteria.  Also available for panTro2 (chimpanzee).  Not available for hg19.
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr10&position=chr10:69713986-69714099&g=ntSeqReads">Neandertal 
 Sequence Reads</A>: Shows Neandertal sequence reads mapped to the human genome.
 Also available for panTro2 (chimpanzee).
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chr10&position=chr10:69713986-69714099&g=ntModernHumans">Alignments 
 of Sequence Reads from 5 Modern Humans</A>: Shows human sequence reads of
 five individuals mapped to the human genome.  These data were used in the 
 S score and Candidate Gene Flow analyses (above).  Not available for hg19.
 <LI>
 <A HREF="../cgi-bin/hgTrackUi?db=hg18&c=chrM&position=chrM&g=ntMito">Neandertal 
 Mitochondrial Sequence</A>: Shows the alignment of a complete Neandertal 
 mitochondrial sequence from a prior publication (Green <em>et al.</em>, 2008) 
 to a modern human mitochondrial sequence.
 </UL>
 
 <!-- Display image in lefthand corner -->
 <TABLE ALIGN=LEFT BORDER=0 WIDTH=315>
   <TR><TD ALIGN=LEFT>
       <IMG SRC="Krause_DSC_0675_small.JPG" HEIGHT=356 WIDTH=536 ALT="Vindija Cave, Croatia">
   </TD></TR>
   <TR><TD ALIGN=LEFT> 
       <FONT SIZE=-1>Entrance of the Vindija Cave, Croatia<BR> 
       </FONT>
       <FONT SIZE=-2> 
         Copyright: Johannes Krause, <A HREF="http://www.eva.mpg.de/neandertal/"
     	TARGET=_BLANK>Max Planck Institute for Evolutionary Anthropology</A>.
       	All rights reserved.<BR>
       </FONT>
   </TD></TR>
 </TABLE>
 
 <!-- Display righthand image -->
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   <TR><TD>
       <IMG SRC="Vindija_bones.jpg" HEIGHT=413 WIDTH=300 ALT="Bones from Vindija Cave">
   </TD></TR>
   <TR><TD> 
       <FONT SIZE=-1>The researchers obtained the majority of the DNA used for 
 	their study
 	from the bone fragments of three female Neandertals that were excavated
 	in the Vindija Cave in Croatia.<BR> 
       </FONT>
       <FONT SIZE=-2> 
         Copyright: <A HREF="http://www.eva.mpg.de/neandertal/"
     	TARGET=_BLANK>Max Planck Institute for Evolutionary Anthropology</A>.
       	All rights reserved.<BR>
         <P></P>
       </FONT>
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                           <TBODY>
                             <TR><TD><a name="Downloads"></a><font size="4"><b>&nbsp;
 				Downloads</b></font> 
 			    </TD></TR>
                           </TBODY>
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                                 <P>
 Data files for tracks at UCSC can be downloaded at the locations below.
-Files that end with .sql and .txt.gz are dumped from our MySQL
+Files that end with .sql and .txt.gz are dumped from our MariaDB
 database; .sql files name the data fields of each row, and .txt.gz
 files contain all rows with tab-separated fields.  
 All database dump files have a first column &quot;bin&quot; that can
 be ignored (it is for database query speedup).  
 
 Files that end in .bam and .bai contain compressed sequence alignments
 and index files in the <A
 HREF="http://samtools.sourceforge.net/SAM1.pdf" TARGET=_BLANK>BAM</A>
 format.  
 The free software packages <A HREF="http://samtools.sourceforge.net/"
 TARGET=_BLANK>samtools</A> and 
 <A HREF="http://picard.sourceforge.net/"
 TARGET=_BLANK>PICARD</A> are useful for viewing and manipulating BAM 
 files.
 
 The .bw suffix denotes the 
 <A HREF="../goldenPath/help/bigWig.html">bigWig</A> format, which stores 
 a numeric signal for genomic positions.</P>
 <P>
 All links below can be fetched using 
 <A HREF="http://rsync.samba.org/" TARGET=_BLANK>rsync</A>; replace 
 &quot;ftp://&quot; with &quot;rsync://&quot; in the links below.
 <UL>
 <LI><B>Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage:</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.txt.gz</A><BR>
 Human (hg19):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.txt.gz</A><BR>
 </LI>
 <LI><B>Selective Sweep Scan (S) on Neandertal vs. Human Polymorphisms:</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/bbi/ntSssZScorePMVar.bw"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/bbi/ntSssZScorePMVar.bw</A><BR>
 Human (hg19):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/bbi/ntSssZScorePMVar.bw"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/bbi/ntSssZScorePMVar.bw</A><BR>
 </LI>
 <LI><B>Selective Sweep Scan (S): 5% Smallest S scores:</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.txt.gz</A><BR>
 Human (hg19):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.txt.gz</A><BR>
 </LI>
 <LI><B>SNPS Used for Selective Sweep Scan (S):</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.txt.gz</A><BR>
 Human (hg19):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.txt.gz</A><BR>
 </LI>
 <LI><B>Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans:</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.txt.gz</A><BR>
 Human (hg19):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.txt.gz</A><BR>
 </LI>
 <LI><B>Neandertal Sequence Contigs Generated by Genotype Caller:</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam.bai</A><BR>
 Chimpanzee (panTro2):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam.bai</A><BR>
 </LI>
 <LI><B>Neandertal Sequence Reads:</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam.bai</A><BR>
 Human (hg19):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam.bai</A><BR>
 Chimpanzee (panTro2):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam.bai</A><BR>
 </LI>
 <LI><B>Alignments of Sequence Reads from 5 Modern Humans:</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
 </LI>
 <LI><B>Neandertal Mitochondrial Sequence (2008):</B><BR>
 Human (hg18):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.txt.gz</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/ntMito/ntM.fa"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/ntMito/ntM.fa</A><BR>
 Human (hg19):<BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.sql"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.sql</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.txt.gz"
 >ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.txt.gz</A><BR>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/ntMito/ntM.fa"
 >ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/ntMito/ntM.fa</A><BR>
 </LI>
 </UL>
 </P>
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                           <TBODY>
                             <TR><TD><a name="Credits"></a><font size="4"><b>&nbsp;
 				Credits</b></font> 
 			    </TD></TR>
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                                 <P>
 				The Neandertal Genome Project was carried out 
 				at the 
 				<A HREF="http://www.eva.mpg.de/neandertal/" 
 				TARGET=_BLANK>Max Planck Institute for 
 				Evolutionary Anthropology</A> under the 
 				direction of Svante P&auml;&auml;bo and made 
 				possible by a grant from the Presidential 
 				Innovation Fund of the Max Planck Society.</P>
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                           <TBODY>
                             <TR><TD><a name="References"></a><font size="4"><b>&nbsp;
 				References</b></font> 
 			    </TD></TR>
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                               <TD>
 <H3>Neandertal Genome Analysis Consortium (2010):</H3>
 <P>
 Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N,
 Li H, Zhai W, Fritz MH  <em>et al.</em>
 <A HREF="http://www.sciencemag.org/cgi/content/full/328/5979/710"
 TARGET=_blank>A draft sequence of the Neandertal genome</A>.
 <em>Science</em>. 2010 7 May;328(5979):710-22.
 </P>
 <P>
 Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, 
 Maricic T, Johnson PLF, Xuan Z <em>et al.</em>
 <A HREF="http://www.sciencemag.org/cgi/content/full/328/5979/723"
 TARGET=_BLANK>Targeted investigation of the Neandertal genome by array-based 
 sequence capture</A>.
 <em>Science</em>. 2010 7 May;328(5979):723-5.
 </P>
                               
 <H3>Previously published mitochondrial genome of Vi33.16 (2008):</H3>
 <P>
 Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, 
 Good JM, Maricic T, Stenzel U, <em>et al.</em>
 <A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602844/?tool=pubmed" TARGET=BLANK>A complete 
 Neandertal mitochondrial genome sequence determined by high-throughput 
 sequencing.</A>
 <em>Cell.</em> 2008 Aug 8;134(3):416-26.
 </P>
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                           <TBODY>
                             <TR><TD><a name="Conditions"></a><font size="4"><b>&nbsp;
 				Conditions of Use</b></font> 
 			    </TD></TR>
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 				The sequence and annotation data displayed in 
 			  	the Genome Browser are freely available for 
 				academic, nonprofit, and personal use (see 
 				<A HREF="../#Conditions">Conditions of Use</A>).
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