1000genomes_browser_quickstart
1000 Genomes Browser Orientation and Pilot Data https://www.sodocs.net/doc/0f653130.html, Based on Pilot Project Data
Paul Flicek
European Bioinformatics Institute
3 November 2010
Overview
??Based on version 54 of Ensembl code and NCBI36 version of the human genome assembly
??Contains all of the gene information normally present in Ensembl
–?Gene and transcript annotation, external references, sequence data ??Incorporates essentially all of the 1000 Genomes Pilot data
–?Some details and additional configuration options will be added over the coming weeks
??Please send questions to info@https://www.sodocs.net/doc/0f653130.html,
??1000 Genomes full project data will be released in a new browser as the data becomes available
1000 Genomes Browser Home Page
Main location view
1000 Genomes SNPs populations and exon capture data can be
Tracks for all SNPs from dbSNP build 129
SNP Information ??SNPs are clickable which brings
up a small window with basic
information
??The SNP properties link leads
to a dedicated page for the SNP
with detailed information
(including information imported
from dbSNP)
SV Information
??Structural variants of specific types are selectable via the “configure this page” link
??Pop-up menus from clicking on the variant list whether the variant has been validated
Resequencing alignment
??View any region of the genome
in alignment with reference for
the 6 high coverage trio
individuals
??Assumption made that if there
is sequence coverage and not
a SNP called, the base is the
same as the reference
–?Not a de novo assembly
??Use Resequencing link on
the left side of pages to access
view
Resequencing alignment
options
Resequencing alignment
output
??SNPs are annotated
–?Heterozygous SNPs with
ambiguity codes
??Currently based on data from HapMap and Perlegen populations
??Populations selectable from
drop down tab
Data Export
??Summary data from
the region being
viewed can be
exported
??Additional export
configuration options
coming soon
More variation displays Transcript Page
Credits
??Eugene Kulesha, Glenn Proctor
??Natassa Spiridou
??Will McLaren, Fiona Cunningham
??Laura Clarke, Holly Zheng-Bradley, Rick Smith ??info@https://www.sodocs.net/doc/0f653130.html,