Public "whole genome" chrY data analysis
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Summary of terms of use: The contents of this spreadsheet, including sample classification and variant details, are available to be used and shared freely, provided: 1) this spreadsheet (and its contributors, as appropriate) are acknowledged; 2) the relevant individuals (listed below) are contacted to inform them prior to use of any of the spreadsheet contents for any academic or commercial work, analysis, product, etc. (i.e. please contact the appropriate individuals below if you intend to make use of this analysis); and 3) the underlying datasets (e.g. Personal Genome Project or 1000 Genomes Project) are cited or acknowledged, as appropriate. The analysis is provided on an as-is basis, without guarantee for accuracy or completeness. If you are interested in contributing, collaborating, making corrections, or discussing content, you are encouraged to contact one or more of the individuals listed below.
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Please see the following for further details:https://sites.google.com/site/yanalysis/
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Current active contributors (last update 2015/10/25)Areas of focusContact info
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A.G.Hg-R, Hg-I, Hg-Oandygrierson22 at gmail dot com
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Bonnie SchrackHg-A, Hg-B, Hg-Jbschrack1 at comcast dot net
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Chris RottensteinerHg-J2achrisr.gen at gmail dot com
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David ReynoldsHg-Rdna at daver dot info
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Greg Magoongeneral (coordination, etc.), Hg-R, Hg-I, sample classificationgregm4584 at gmail dot com
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Ray Banksroot area, Hgs C, D, E, F, G, H, K, L, M, N, P, Q, S, Tdnagrouper2 at gmail dot com
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R.R.Hg-R
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Roman SychevHg-I, Hg-R, Hg-J2b
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Steve FixHg-E-M215fixdnaproject at shentel dot net
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V.MasHg-J1victar at genogenea dot come
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Vince TilroeHg-R, Hg-J2bvtilroe at gmail dot com
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John SloanHg-R-U198 (R-S29)sloanydna at aol dot com
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Contributors also gratefully acknowledge and appreciate helpful discussions with hundreds of individuals participating in the broader genetic genealogy community
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Past contributors
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P.O.Hg-R
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asdgood
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G.H.Hg-O
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L.M.Hg-R
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Dataset citations
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1000 Genomes Projecthttp://www.1000genomes.orgAn integrated map of genetic variation from 1,092 human genomes, McVean et Al, Nature 491, 56–65 (01 November 2012) doi:10.1038/nature11632
http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html
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Personal Genome Projecthttp://www.personalgenomes.orgBall, Madeleine P., et al. "A public resource facilitating clinical use of genomes." Proceedings of the National Academy of Sciences 109.30 (2012): 11920-11927.
http://www.pnas.org/content/109/30/11920.long
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Associated publications
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Rocca RA, Magoon G, Reynolds DF, Krahn T, Tilroe VO, Op den Velde Boots PM, Grierson AJ (2012) Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach. PLoS ONE 7(7): e41634. doi:10.1371/journal.pone.0041634http://dx.doi.org/10.1371/journal.pone.0041634
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Gregory R Magoon, Raymond H Banks, Christian Rottensteiner, Bonnie E Schrack, Vincent O Tilroe, Terry Robb, Andrew J Grierson (2013) Generation of high-resolution a priori Y-chromosome phylogenies using “next-generation” sequencing data. bioRxiv preprint doi:10.1101/000802http://dx.doi.org/10.1101/000802
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README
Summary statistics
U106 Samples
U106 Candidate Variants
L21 Samples
L21 Candidate Variants
U152 Samples
U152 Candidate Variants
R1a Samples
R1a Candidate Variants
DF27 Samples
DF27 Candidate Variants
Misc. P312 Samples
Misc. P312 Candidate Variants
Unassigned P310 Samples
Misc Hg R Samples
Misc R1b Variants
R2a Candidate Variants
Misc (xR) Samples/partial Hgs
A Samples
A0 Candidate Variants
A1a Candidate Variants
A1a Candidate Variants (Cont.)
A1b Candidate Variants
B Samples
BT Candidate Variants
B Candidate Variants
C Samples
C Candidate Variants
D Samples
D Candidate Variants
E Samples
E Root Candidate Variants
E Candidate Variants
E-M33 Variants
E-U175 Samples
E-U175 Candidate Variants
E-M191 Samples
E-M191 Candidate Variants
F Samples
G Samples
G Candidate Variants
G-L140 Candidate Variants
H Samples
H Candidate Variants
H-Z5857 Candidate Variants
I1 Samples
I1 Candidate Variants
I2 Samples
I2 Candidate Variants
IJK Samples
J Samples
J1 Candidate Variants
J2 Candidate Variants
K Samples
L Samples
L Candidate Variants
LT Variants
M Samples
N Samples
N Candidate Variants
NO Candidate Variants
NO Upstream samples
O samples
O Candidate Variants
P Samples
Q Samples
Q Candidate Variants
S Samples
T Samples
T Candidate Variants
Ancient Hominid Samples
Unassigned Samples
Root level Candidate Variants
Phase III Affy data staging
CAGI mapping
Known SNPs (Build 37)