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Neandertal Genome Analysis Consortium Tracks at UCSC
Artist's rendering of Neandertal man, from Neandertal museum in Mettmann, Germany Copyright: Johannes Krause, Max Planck Institute for Evolutionary Anthropology. All rights reserved.
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 et al. in Science 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. This portal provides access to the sequence data and alignments to the reference human genome (NCBI Build 36/hg18, GRCh37/hg19) as well as the reference chimpanzee genome (CGSC 2.1/panTro2) and several associated analyses (see Downloads and References). The following annotations are available on the human hg18 and hg19 genome assemblies, except as noted: Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage: 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. Selective Sweep Scan (S) on Neandertal vs. Human Polymorphisms: 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. Selective Sweep Scan (S): 5% Smallest S scores: 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. SNPS Used for Selective Sweep Scan (S): Shows single nucleotide polymorphisms (SNPs) on which the S score (above) was calculated. Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans: 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. Neandertal Sequence Contigs Generated by Genotype Caller: 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. Neandertal Sequence Reads: Shows Neandertal sequence reads mapped to the human genome. Also available for panTro2 (chimpanzee). Alignments of Sequence Reads from 5 Modern Humans: 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. Neandertal Mitochondrial Sequence: Shows the alignment of a complete Neandertal mitochondrial sequence from a prior publication (Green et al., 2008) to a modern human mitochondrial sequence.
Entrance of the Vindija Cave, Croatia Copyright: Johannes Krause, Max Planck Institute for Evolutionary Anthropology. All rights reserved.
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. Copyright: Max Planck Institute for Evolutionary Anthropology. All rights reserved.
Downloads
| 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 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 "bin" 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 BAM format. The free software packages samtools and PICARD are useful for viewing and manipulating BAM files. The .bw suffix denotes the bigWig format, which stores a numeric signal for genomic positions. All links below can be fetched using rsync; replace "ftp://" with "rsync://" in the links below. Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage: Human (hg18): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.txt.gz Human (hg19): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.txt.gz Selective Sweep Scan (S) on Neandertal vs. Human Polymorphisms: Human (hg18): ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/bbi/ntSssZScorePMVar.bw Human (hg19): ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/bbi/ntSssZScorePMVar.bw Selective Sweep Scan (S): 5% Smallest S scores: Human (hg18): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.txt.gz Human (hg19): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.txt.gz SNPS Used for Selective Sweep Scan (S): Human (hg18): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntSssSnps.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntSssSnps.txt.gz Human (hg19): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntSssSnps.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntSssSnps.txt.gz Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans: Human (hg18): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.txt.gz Human (hg19): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.txt.gz Neandertal Sequence Contigs Generated by Genotype Caller: Human (hg18): ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam.bai Chimpanzee (panTro2): ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam.bai Neandertal Sequence Reads: Human (hg18): ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam.bai Human (hg19): ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam.bai Chimpanzee (panTro2): ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam ftp://hgdownload.cse.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam.bai Alignments of Sequence Reads from 5 Modern Humans: Human (hg18): ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai Neandertal Mitochondrial Sequence (2008): Human (hg18): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntMito.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ntMito.txt.gz ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/ntMito/ntM.fa Human (hg19): ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntMito.sql ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ntMito.txt.gz ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/neandertal/ntMito/ntM.fa |
Credits
| The Neandertal Genome Project was carried out at the Max Planck Institute for Evolutionary Anthropology under the direction of Svante Pääbo and made possible by a grant from the Presidential Innovation Fund of the Max Planck Society. |
References
| ### Neandertal Genome Analysis Consortium (2010): 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. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PLF, Xuan Z et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science. 2010 7 May;328(5979):723-5. ### Previously published mitochondrial genome of Vi33.16 (2008): 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. |
Conditions of Use
| The sequence and annotation data displayed in the Genome Browser are freely available for academic, nonprofit, and personal use (see Conditions of Use). |