To learn more about our genome sequence results:

Data Release

Sequencing Results

Technology Overview

Complete Genomics has made available several data sets from NA19240, an International HapMap project Yoruban female sample. This sample was sequenced using Complete Genomics’ third-generation human genome sequencing technology. High-level summary information describing the sequencing results for this sample may be reviewed in the NA19240 Data Sheet. For more detailed data and results, see the Variation Data, NA19240 Chromosome Data Set, Science Paper Data Sets, and Complete NA19240 Data Set sections below. Documentation regarding the file formats is available here.

Complete Genomics has posted recently updated NA19240 results which are derived from the same source data used in our Science publication (Science 327 (5961), 78. [DOI: 10.1126/science.1181498]). While the published data set is of excellent quality, Complete Genomics has made improvements to our service since that time, in particular by providing additional data analysis results. These data have been reanalyzed using a newer version of our pipeline software (v1.7.0), thus the data is now provided in an updated file format. Please note: Complete Genomics requests that the version number of the assembly software be included in any publications and presentations referencing these data.

The variation file for NA19240 contains a complete description of this genome as compared to the NCBI reference genome (Build 36). Every base of this genome in reference genome coordinate space is described as variant, same as reference, or as no-called base. In addition, annotation files are available showing the sequence of NA19240 at sites of known polymorphisms (from dbSNP 129) and in the coding regions of known genes. A summary table of functional changes categorized by transcript is also available. The current software version available for this data set is 1.7.3.

1. Documentation:
   DataFileFormats.pdf (784 KB) contains detailed descriptions of Complete Genomics data formats. Note that not all data described in the DataFileFormats.pdf is available for download below.
    
2. Variations:
   GS000000320-ASM.tsv.bz2 (318,975 KB): Called sequence relative to NCBI reference including all base calls and no-calls from NA19240.
    
3. Annotations:
   dbSNPAnnotated-GS000000320-ASM.tsv.bz2 (327,016 KB): For each entry in dbSNP 129, states call in NA19240.
   
   gene-GS000000320-ASM.tsv.bz2 (112,500 KB): Functional annotation of individual variants called in NA19240 (nonsynonymous SNPs, frameshifting indels, etc)
   
   gene-var-summary-GS000000320-ASM.tsv (2,318 KB): For each transcript, summarizes the number of variations with certain functional impacts (counts of nonsynonymous SNPs, etc.)
   
   summary-GS000000320-ASM.tsv (2 KB): Overall information and statistics for this sequencing project.
    

A complete data set for NA19240 chromosome 21 is also available for download. It includes a subset of the variant files described above, and in addition the assemblies, mapping data, reads and quality scores, coverage data and other computed results. This data set is useful for understanding the data structure and file formats of Complete Genomics’ sequence data, for downstream software and analysis development, as well as for a variety of other applications.

Data included in this release are broken into five portions for ease in downloading..

1. GS19240-173-21-pt1-ASM.tar(564 MB): Contains the contents of the ASM and LIB folders. These folders contain the complete set of derived results from the genome sequencing: variant calls, annotations, coverage information and assemblies. This also includes the individual reads, quality scores, and initial mapping results for a single lane, primarily as an example.
2. GS19240-173-21-pt2-MAP.tar(3 GB): Contains individual reads, quality scores, and initial mapping results for about a third of the data set by size.
3. GS19240-173-21-pt3-MAP.tar(3 GB): Contains individual reads, quality scores, and initial mapping results for roughly another third of the data set.
4. GS19240-173-21-pt4-MAP.tar(2.997 GB): Contains all remaining individual reads, quality scores, and initial mapping results, also roughly a third of the data set.
5. GS19240-173-21-DOC.zip(1.75 GB): Contains the documentation for this data set.

The read and variation data from the data from the three human genomes (NA19240, NA07022, and NA20431/PGP1) from the Science publication and based on the CGI software in use as of that submission has been submitted to the Short Read Archive at NCBI (SRA008092).

The complete dataset of sample NA19240 for the entire genome is also available by request. This data set (~400 Gb) is provided in the format and structure of a typical customer result.