1000 Genomes Browser: Frequently Asked Questions...

1. Why does the genotype table sometimes get out of sync with the region shown in the Sequence Viewer?

UPDATE: This is fixed. If you still see this behavior, please report it using the 'Write to Help Desk' link at the bottom of the page.

This was a known bug in the initial release of this tool (v 1.0 beta). This should be corrected with the v 1.1 update, which should be public by the end of March 2012. If you continue to see problems with the page, please use the 'Write to the Help Desk' link at the bottom of the page to report the problem.

2. Why can't I download a VCF file when using Internet Explorer?

UPDATE: This is fixed. If it's still a problem, please report it using the 'Write to the Help Desk' link at the bottom of the page.

There is a file extension conflict in windows, as .vcf is also the file extension used for vCards (electronic business cards sometimes used by Outlook). We are working on a fix for this problem, but you should be able to download the file using another browser.

3. Can I load my own variant data to this site?

Yes you can. Upon expanding the 'Your Data' widget located on the left side of the page, you can select files for upload or drag them into the widget. Alternatively, select the 'Configure' link in the upper right hand corner of the Sequence Viewer widget. When the new dialog opens, select the top tab labeled 'Custom Data', then select the 'Data File' option. We are currently support a variety of file types, including VCF and GVF , two commonly used formats for describing variation data. For more information on uploaded data, please see the Help page .

4. Where do the BAM files supporting this browser come from?

UPDATE: August, 2016. Phase 1 BAMs are no longer available in the browser.

The BAM files used in this browser were generated by the 1000 Genomes project as part of the phase 1 and phase 3 analyses.

5. Why do some samples have more than one BAM file?

UPDATE: August, 2016. Phase 1 BAMs are no longer available in the browser.

Most subjects were sequenced as part of the low-coverage project and the exome project. In phase 1, a few subjects were also sequenced as part of a high-coverage effort. Each project will produce at least one BAM file. Additionally, in phase 1, some data was aligned using different aligners; in these cases we will provide access to the BAMs for each alignment protocol.

6. Can I report bugs or make feature requests?

Yes! At the bottom of most NCBI web pages is a link with the words "Write to the Help Desk". When you click on this link a new window will open and you will be presented with a form to fill out. Please fill this out and we'll do our best to address your problem.

7. Why do some locations in the genotype table not have dbSNP or dbVar/DGVa IDs?

The 1000 Genomes project is large and complex and not all data is deposited to the public repositories at the same time. At the time of the initial v3.4 browser release, not all variants in the 1000G phase 3 callset VCFs had these database ids. When these become available, the browser will be updated with the data.. We anticipate that we will be able to provide database identifiers for all sites in a later release cycle.

8. There is a variant call shown in the genotype table but I don't see evidence for a base change when I view the alignments.

The 1000 Genomes project used a variety of variant callers to produce the final set of variants. Some of these callers used imputation to make SNP calls in regions with no or low coverage. You can get more information about the 1000 Genomes analysis methods here .

9. Why do some columns in the genotype table sometimes get a gray background?

Columns showing data that are outside the range that is currently being viewed get a gray background in order to make it clear that these SNPs are outside of the current viewing range.

10. Should I use the phase 1 or phase 3 callset data?

UPDATE: August, 2016: The browser no longer supports the phase 1 callset data.

The phase 3 callset is considered the final data release from the 1000G project and is the callset whose use we recommend. Phase 1 was a pilot in which different sequencing and alignment approaches were tested on a limited number of Subjects. Methodologies used for phase 3 are more standardized. In addition, phase 3 contains data from more populations. For more information on project details, see the 1000 Genomes website . We are maintaining support for the phase 1 callset data for a limited time, to give users time to transition to the new callset. There are 59 Subjects in the phase 1 callset that were excluded from phase3 because their low-coverage and/or exome data did not meet the criteria for phase 3.

11. Why are there no genotypes for the mitochondrial chromosome in the phase 3 callset genotype table?

Genotype calls on chr. MT have not yet been released for the phase 3 callset. When these become available, the browser will be updated with the data.

12. What is the "related samples" Subjects widget filter?

These are Subjects from the 1000 Genomes project whose alignment and genotype data were excluded from allele frequency (AF) calculations for a callset because they share a close relationship with other 1000 Genomes subjects and would therefore bias the AF. Within the genotypes table, Subjects defined as "related samples" are shown in red italicized font. Note: At the time of the initial v3.4 browser release, only BAM tracks, but not genotypes, for phase 3 related samples are available in the browser. These will soon be added in a browser update. Update, March 2015: Genotypes for related samples have been added to the Genotypes table.

13. Why are some Subjects with BAM tracks missing from the Genotypes table?

These are the related samples from the phase 3 callset. They will be added to the Genotypes table in a browser update. See FAQ #12 for more information. Update, March 2015: Genotypes for related samples have been added to the Genotypes table.

14. Why do some of the alignments have colored backgrounds?

When zoomed to the base pair level, alignments have a gray background by default. Alignments with a solid pink background represent PCR duplicates, while reads with a solid deep-red background are PCR errors.

15. Why do the coordinates for some variants differ between the Search results and the Genotype table?

Coordinates for indel variants may be different between Search results and the Genotype table due to differences in reporting methods. The Genotypes table reports the VCF position for that variant, while the Search results reports the the variant base position, which corresponds to the dbSNP record. For example, rs71022512, which refers to a single base indel is reported in the Genotypes table as NC_000010.10: 89623860, while is listed in the Search results at NC_000010.10: 89623861. For more information on variant reporting in VCF, see the VCF specs .

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Last updated: 2017-12-05T20:59:00Z