YH genome was assembled based on 3.3 billion reads generated by Illumina Genome Analyzer. We achieved 117.7G nucleotides data and the genome was sequenced to 36-fold average coverage. By aligning the short reads with SOAP, 102.9G nucleotides are mapped onto the NCBI reference genome and 99.97% of the genome has been covered. The raw sequences, aligments, consensus genome, variants and relevant tools are released for public use. And the documents about donor consent and sample collection are avialable at the bottom of this page.

Note:

BGI-shenzhen FTP server has been change to ftp://public.genomics.org.cn
Please use the New site.
We suggest to use ftp tools to download the files,such as FileZilla on Windows, wget on Linux etc.

Raw Data   

  a)    Single_end_data  FTP1  FTP2

  b)    Pair_end_data  FTP1  FTP2

Processed Data

1 YH genome sequence

a) Fasta by chromosome   FTP1

These files are YH chromosome sequences in FASTA format. In order to make them easy to use, all indels are not taken into the sequences, so the sequences have the same coordinates as UCSC build hg18, which is essentially same to NCBI human v36.1.

b)Fasta.qual by chromosome  FTP1

The files contain quality information of consensus bases.

c) Total genome : YH Fasta  YH Fasta.qual
The files are concatenated from above FASTA sequences and the quality information.

2 YH variants and annotations

These files are variants results extracted from SOAP alignments.

• SNPs:YH-SNPs.gff Download  Open
• Indels :YH-Indels.gff Download  Open
• Structural Variations : YH-sv.gff Download  Open

README: GFFDefinitions.doc

3 Short read alignments

• Alignment by chr  FTP1
These files are alignments in format of SOAP output.

README: AlignmentDTD.doc

4 Genotyping

• Genotyping  FTP1

README:README

5 Original Illumina 1M Duo genotyping result.

• FTP1

These are the original base-calls from Illumina 1M Duo bead chip. These include sites that are inconsistent between the two replicates and those failed.

6 Phased haplotype blocks of YH based on HapMap data.

• FTP1

7 YH and NA18507 genome assembly

• FTP1

The sequences of de novo assembly of YH and NA18507

8 Novel sequences

HTTP

•  Novel sequences of YH genome
•  Novel sequences of NA18507 genome
•  MD5 checksum
•  Additional comments on genetic diversity of novel sequences in Ruiqiang Li,Yingrui Li,Hancheng Zheng, Ruibang Luo, et al. 2009. Building the sequencemap of the human pan-genome. Nature Biotechnology (Published online at Dec 7)




FTP

FTP1

Novel sequences detect on de novo assembly of YH and NA18507

9 Predicted genes

• FTP1

Predicted genes on novel sequences of YH and NA18507

10 YH and NA18507 Novel sequences PCR gel picture

• FTP1

11 Sequenceing depth of YH genome's each site

• FTP1

12 YH exome raw data

• FTP1

13 YH SV case

• FTP1

YH SV cases detected by comparison between YH de novo assembly and NA18507

14 African genome SV case

• FTP1

15 Structural variation sets of YH and NA18507 identified by de novo assembly.

• FTP1

16 YanHuang fosmid sequence

• FTP1

17 SOAPSV pipeline

HTTP

• SOAPSV's  Programs and scripts
• SOAPSV's  Documents

About donor consent

These are documents about donor consent to participate.

• Donor consent of the Yanhuang Project-Phase I(in chinese): Download
• IRB Validation: Download
• The Informed Consent forms: Download
• The Protocol: Download