Y-Chromosome Genome Comparison
Errata for 23andME Data Compilation

 

Row number is the line in Adriano’s project spreadsheets where the SNP is listed.

Row 10: P211, i4000162, ChrY:2723707
Haplogroup E1b1a, Karafet (2008) and ISOGG (2010)
All results under Haplogroup E1b1a are incorrect
Values for this SNP should be ignored

Row 260: L245, i4000258, ChrY:5735090, v2 only
23andME lists as rs2565384, ChrY:5735094 (equivalent to L153)
Derived near Q1b-M378
Nomenclature issue, not an issue with the results
Values for this SNP are OK to use
[Contradictory results for this SNP at 23andME and FTDNA led to the discovery that 23andME was reporting the wrong location. Allele values reported as “A” (ancestral for L153) should be treated as if they were “C” values (ancestral for L245). In either case, “G” is the derived value and correct.]

Row 599: P27/P207, i4000186, ChrY:12994387
Haplogroups P/O3a1, Karafet (2008) and ISOGG (2010)
The v1/v2 results are incorrect
Use with caution, ensure data is v2.5/v3

Row 603: P245, rs3853052, ChrY:8693545
Haplogroup R1, ISOGG (2010)
Haplogroup P, Karafet (2008), is refuted by spreadsheet data
Six R2-M124 samples sequence by the GRC are P245-, confirming Hg R1
Results are correct  for P245 (R1)
Values for this SNP are OK to use

Row 682: L150, rs9785831, ChrY: 10618791
Haplogroup R1b1b2a, ISOGG (2010)
Some results are inconsistent. Vince Vizachero stated 31 Mar 2010 on DNA-Forums: “We have received a total of about thirty results for L150, all of them consistent with the placement of L150 on the same branch as L23 and L49. It does not define a distinct paragroup. The one infamous L23+ L150- is apparently the result of cross-amplification of a distinct (previously unmapped) piece of DNA from someplace other than the Y.” He further stated on 21 Sep 2010 (private communication to me): “Most of the time the L150 results are fine.  But in a small percentage of men, the primers and probes pick up a different segment of DNA than usual and return a spurious result.” The Romitti result (L23+ L150-) and the Sutherland result (M269+ L150+) both fall into the “spurious” category and should be disregarded.
Values for this SNP should either be ignored, or used with extreme caution

Row 704: P164, rs17316007, ChrY:12511232
Haplogroup O3a3b2, Karafet (2008) and ISOGG (2010)
Results are inconsistent under O3a3 (v3 status unknown)
Values for this SNP should be ignored

Row 757: P38, i4000186, ChrY:12994387
Haplogroup I, Karafet (2008) and ISOGG (2010)
All results for Haplogroup I are incorrect
Values for this SNP should be ignored

Row 769: P50, i4000258, ChrY:13005250
Haplogroup B2a1a, Karafet (2008) and ISOGG (2010)
Results for Haplogroup B2a1a are incorrect (v3 status unknown)
This SNP is an indel, which as a class are known to be problematic
Values for this SNP should be ignored

Row 906: M379, i4000051, ChrY:13536922
Haplogroup I2b1b, Karafet (2008) and ISOGG (2010)
The v2.5/v3 results for Haplogroup YxG are incorrect
This SNP is an indel, which as a class are known to be problematic
Values for this SNP should be ignored

Row 1809: PK2, i4000240, ChrY:21078608
Haplogroup C3, Karafet (2008) and ISOGG (2010)
Single C3 sample shows ancestral
Could either be an issue with 23andME, or with SNP placement in haplotree
Use with caution, v3 status is unknown

Row 1521: P227, rs4481791, ChrY:19869094
Haplogroup R, Karafet (2008) and ISOGG (2010)
All results for Haplogroup R are incorrect
WTY confirms that P227 is in fact Hg R
Values for this SNP should be ignored

Row 1702: M73, rs2032634, ChrY:20348262
Haplogroup R1b1b1, Karafet (2008) and ISOGG (2010)
The v1 results are incorrect
This SNP is an indel, which as a class are known to be problematic
Use with caution, ensure data is v2/v2.5/v3

Row 1738: M91, rs2032651, ChrY:20366926
Haplogroup A, Karafet (2008) and ISOGG (2010)
v2 results for Haplogroup A are incorrect; v3 status unknown
This SNP is an indel, which as a class are known to be problematic
Values for this SNP should be ignored

Row 1802: PK1, i4000238, ChrY:20992895
Derived near Haplogroup A
Haplogroup A2, Karafet (2008), is refuted by spreadsheet data
Results are correct assuming PK1 (derived near A)
Values for this SNP are OK to use

Row 1954: P188, rs16980610, ChrY:22043750
Derived near Haplogroup O
Haplogroup NO, Karafet (2008) and ISOGG (2008), is refuted by spreadsheet data
Results are correct assuming P188 (derived near O)
Values for this SNP are OK to use

Row 2220: L157, rs17222657, ChrY:17072101
Derived near Haplogroup I1 and under haplogroups R-L21 and R-U152
23andME reported L157+ for Ilmarinen; FTDNA testing showed L157-
Inconsistent results, unknown where the problem is, use with caution

Download Version Definitions

v1 Results
Tests done prior to Sep 2008 used the first generation Illumina chip
Downloads were referred to as v1 results and contained 1358 SNPs

v2 Results
Tests done after Sep 2008 used the second generation Illumina chip
Downloads done from Sep 2008 to Apr 2009 are collectively referred to as v2 results
Oct 2008, “double-letter” calls changed to “single-letter” calls, and heterozygous calls changed to no-calls
Downloads from Sep to Dec 2008 contained 2042 SNPs
221 unreliable SNPs were discontinued on 16 Dec 2008 (listed as “deprecated” in the spreadsheets)
Downloads from Dec 2008 through Apr 2009 contained 1821 SNPs
The v1/v2 results in the project spreadsheets have the sample name listed in black text
Rows 2184 through 3797 of the project spreadsheets will be empty for v1/v2 results

v2.5 Results
Second generation downloads done after 9 Apr 2009 are referred to as v2.5 results and contain 1923 SNPs
Data downloaded after 25 Mar 2010 may have fewer no-call results due to analysis improvements
Rows 2184 through 2237 of the project spreadsheets will have values in them for v2.5 results and rows 2238 through 3797 will be empty
N.B., prior to Dec 2010 some people used “v3” to refer to these results

v3 Results
Tests done after Nov 2010 use the third generation Illumina HumanOmniExpress array
Downloads are referred to as v3 results and contain 3483 SNPs
Rows 2238 through 3797 of the project spreadsheets will have values in them for v3 results

Further information is available at: http://daver.info/ysub/

 

References

International Society of Genetic Genealogy (2011). Y-DNA Haplogroup Tree 2011, Version: 6.00, Date: 1 Jan 2011, http://www.isogg.org/tree/ [Date of access: 5 Feb 2011].

Karafet Tatiana M et al., (2008). New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Genome Research, published online 2 Apr 2008.

Krahn Thomas (2011). Family Tree DNA Y Chromosome Browser, http://ymap.ftdna.com/ [Date of access: 5 Feb 2011].

Reynolds David F (2011). Y-DNA Forums Genome Comparison SNP and Haplogroup List, Date: 5 Feb 2011, http://daver.info/ysub/remarks.xls [Date of access: 5 Feb 2011].

Squecco Adriano (2011). Y-DNA Forums Genome Comparison Zipped Data Files http://webalice.it/asquecco/Y_DNA-Forums.zip [Date of access: 5 Feb 2011].

 

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Last Modification: 5 Feb 2011.