PGP data

From 1000 Genomes & Other Full Y Sequence Data

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Posts: 3
Joined: Fri Nov 09, 2012 12:56 am

YDNA:
R1b-Z343
MtDNA:
H3 (T152C)
PostPosted: Sat Dec 29, 2012 11:49 pm
Some of us who have worked with the 1kG data have been beginning to look at the newest Personal Genome Project data (from Complete Genomics) as well. I've been extracting and posting the MT and chrY data at https://www.box.com/s/xrzzcmyidopke9bqm8uv . Others, including Roman Sychev, Ray Banks, David Reynolds, and Vince Tilroe have been assisting in the process of classifying the samples in our community maintained Google spreadsheet: https://docs.google.com/spreadsheet/ccc ... g_UD#gid=1 . Currently there are fewer than 100 male samples, but it is anticipated that there will eventually be over 1000. I used the latest survey data-dump to determine the country of origin for the paternal grandfathers for the 1153 PGP participants who have indicated male on the survey. Here's how they break down:
Armenia 3
Austria 3
Azerbaijan 5
Bangladesh 1
Belarus 7
Belgium 2
Brazil 2
Bulgaria 2
Canada 15
China 16
Colombia 1
Croatia 3
Cuba 1
Czech Republic 5
Denmark 1
Egypt 2
El Salvador 3
Estonia 5
Ethiopia 1
Finland 4
France 6
Georgia 1
Germany 41
Greece 1
Guyana 2
Hungary 7
India 14
Iran, Islamic Republic of 1
Iraq 1
Ireland 27
Isle of Man 1
Israel 1
Italy 28
Korea, North (Democratic People's Republic of) 1
Korea, South (Republic of) 1
Latvia 1
Lebanon 1
Lithuania 6
Macao 1
Mexico 4
Moldova, Republic of 3
Morocco 1
Netherlands 7
Nigeria 1
Norway 3
Other / don't know / no response 77
Pakistan 2
Peru 1
Philippines 2
Poland 34
Portugal 2
Puerto Rico 7
Romania 9
Russian Federation 20
Serbia 5
Slovakia 5
Slovenia 6
South Africa 2
Spain 8
Swaziland 1
Sweden 3
Switzerland 3
Syrian Arab Republic 4
Turkey 2
Ukraine 18
United Kingdom 49
United States 647
United States Minor Outlying Islands 1
Venezuela 1
Viet Nam 1
Grand Total 1153
User avatar
Posts: 96
Joined: Wed Mar 14, 2012 5:39 pm

YDNA:
N1c1-L1022
MtDNA:
T2b7a1
PostPosted: Fri Jan 04, 2013 12:40 pm
Does anyone knows of any "Genome browser" that works with these .tsv files? I just want to check some individual Y-SNP in the data.

Posts: 3
Joined: Fri Nov 09, 2012 12:56 am

YDNA:
R1b-Z343
MtDNA:
H3 (T152C)
PostPosted: Mon Jan 07, 2013 3:24 am
Stenhög wrote:Does anyone knows of any "Genome browser" that works with these .tsv files? I just want to check some individual Y-SNP in the data.

The TSV files can be opened in Notepad or Excel and individual results can be read manually if you know what to look for. Each row contains a range of b37 positions, and lists, for example, whether there is a no-call or a SNP or whether the sequence is identical to the reference sequence. Here is a FAQ from Complete Genomics that describes some of the details of these "Variant files" which constitute most of the Complete Genomics .tsv files on the PGP website: http://www.completegenomics.com/FAQs/Va ... ll-Indels/

I'm not sure if these files can be interpreted by any Genome Browsers.

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