Return to Haplogroup R

Frequently Mutating SNPs are SNPs that appear many times in many places either in one or more haplogroups. They are inconsistent and not useful for genealogical purposes.

• L128/PF3499 - listed 13 May 2014.
• L147 - Listed 14 May 2014.
• CTS3849.1/S4628.1 - Listed 14 August 2015.

NOTES:

• Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in the order of discovery, and separated by "/". Examples: M207/UTY2, M306/S1, M173/P241, SRY1532.2/SRY10831.2, L23/S141, L48/S162, L11/S127, P310/S129, P311/S128, M405/S21/U106, M467/S29/U198, DYS439/L1/S26, P312/S116, M167/SRY2627, S28/U152, L2/S139, L20/S144, L21/S145, M222/USP9Y+3636.
• The position of L196 is undertain with respect to the position of Z49
• L405/L584 (ChrY:27141305) is a triallelic SNP with allele values "A", "C", and "T". A value of "A" indicates haplogroup Y(xP) and is referred to as L405-. A value of "C" indicates haplogroup P and is referred to as L405+ and a value of "T" indicates haplogroup R1b1a2a1c and is referred to as L584+.
• L342.2 is known to co-mutate with L319.4, L348.3 and L349.2 in haplogroup R1a; all should be derived if any one of them is. Listed 7 Aug 2011.
• Due to lack of positive control samples for M56, M157.1, M64.2, M87, M204, P98, PK5, and M434, the positions of those private or uncommon SNPs in the haplotree are uncertain with respect to the positions of Z93, Z280, and L176.1/S179.1.
• P25 is an unreliable SNP with a 2% reversion rate within R1b1. It should not be used by itself to classify individuals. For further details see Adams et al (2006) and Discussion of P25
• L49 is a recurrent mutation in Haplogroup R and may be generally unstable in Haplogroup R. In haplogroup R1b1a2a, L49.1 is phylogenetically equivalent to L23. In haplogroup R1a1a1, L49.2 is located under M417. In haplogroup R2a, L49.3 is located at or near P267.
• SNP SRY1532/SRY10831 appears twice on the Y-DNA Haplogroup tree. It is first seen as a mutation SRY1532.1/SRY10831.1 which is reported as a positive in BT and then reappears as a back mutation SRY1532.2/SRY10831.2 which is reported as a negative in R1a.
• Thomas Krahn has developed a new primer for DYS439-Null (aka L1, S26) that gives a score of 12 rather than null.
• Thanks to Jim Wilson and Thomas Krahn for their consultation on Haplogroup R.
• Data from the 1000 Genomes Project suggests that Z220 is downstream from Z209 and Z278 is downstream of Z216. Listed 26 June 2012.
• L195/S354, L144/S175 are STR mutations that happen back and forth so have been removed from the tree. Listed 26 November 2014.
S781 is associated with descendants of Sir John Stewart of Bonkyll who died at the Battle of Falkirk on 22 July 1298. Testers were from many different Stewart/Stuart lines, including Ardsheal, Fasnacloich, Lennox and Buccleuch. Listed 9 October 2015.
• P25_1, P25_2, P25_3 was long listed on the tree but does not meet quality guidelines on 20 January 2016.


• R1a mutations previously on tree but found so far only in one man or in closely related men:
• M56, M64.2/Page44.2, M87, M157.1, M204, M434, P98 and PK5 are downstream of M417. Listed 19 July 2012.
• M334 is downstream of M458. Listed 19 July 2012.
• L175/S467 is downstream of L176.1/S179.1. Listed 19 July 2012.
• BY185.2/SUR33.2, BY186.2/SUR34.2, BY187.2/SUR35.2, BY189.2/SUR41.2, BY190.2/SUR42.2, BY191.2/SUR43.2, BY192.2/SUR44.2, BY193.2/SUR45.2 are located at approximately Z2123. Listed 15 November 2014.
• FGC11892/YP326 is associated with descendants of John the Good, Lord of the Isles (1336–1386), chief of Clan Donald. Listed 9 October 2015.


• R1b mutations previously on tree but found so far only in one man or in closely related men:
• L5 is located downstream of R-U106. Listed 6 Apr 2006.
• S50 is located at approximately R-M269. Listed 6 Apr 2006.
• L50/S136 is located at approximately R-L23. Listed 28 Oct 2010.
• L179 and L180 are located downstream of Z6. L179 and L180 were found in a single individual, and are likely phylogenetically equivalent. Listed 21 Mar 2011.
• L3/S216 is located at approximately R-L562. Listed 10 Jul 2011.
• L135, L209are located at approximately R-L2. Listed 21 Mar 2011.
• L7, L95, L171, L173 and L194 are located at approximately R-P312. Listed 21 Mar 2011.
• L141.2 and S44 are located at approximately R-U152. Listed 6 Aug 2011.
• L626 is located under L627. Listed 6 Aug 2011.
• L625 is located under R-L626. Listed 6 Aug 2011.
• M65 is located downstream of R-P312/S116. The position of private SNP M65 is uncertain with respect to the positions of Z196, L238/S182, DF19 and DF27. Listed 26 June 2012.
• M126 and M160 are located downstream R-S28/U152. The positions of M126 and M160 are uncertain with respect to the positions of L2, Z36, and Z56. Listed 26 June 2012.
• M228.2 is located downstream of R-L21/M529/S145. Listed 26 June 2012.
• M37 is located downstream of R-L21/M529/S145. The position of private SNP M37 is uncertain with respect to the positions DF23/S193, DF1/L513, L96, L159.2/S169.2, Z253, DF21/S192, L371, and DF41. Listed 26 June 2012.
• L319.1 is located under R-DF13. Listed 8 July 2012.
• L302/S464 is located under R-DF49. Listed 8 July 2012.
• L9, L10 are located under R-L513. Listed 8 July 2012.
• L894 and L895 are located downstream of R-L1066. Listed 8 July 2012.
• L696 is downstream of Z326. Listed 18 July 2012.
• L653 is downstream of Z18. Listed 18 July 2012.
• P107 is downstream from U106. Listed 9 August 2012.
• L6 is is downstream from U106. Listed 9 August 2012.
• L325 is downstream from Z18. Listed 9 August 2012.
• V8.1 is downstream from V88 and parallel to M18. Listed 9 August 2012.
• V7 is downstream from V35. Listed 9 August 2012.
• L127.2 is located downstream from L128. Listed 18 August 2012.
• L259/S266 is located downstream from Z301. Listed 18 August 2012.
• M157.2 is located downstream from Z6. Listed 18 August 2012.
• L693 is located downstream from L48. Listed 19 August 2012.
• S420 is located downstream from S425; associated with Wilson surname. Listed 13 September 2012.
• S3068 is located downstream of S302, S303, S421, and S422, but is above S420; associated with Wilson surname. Listed 23 February 2014.
• S303, S421 are downtream from S425; associated with Wilson surname. S421 occured after S422+S302. S303 occurred after S421. Listed 23 February 2014.
• FGC3263 is located downstream from FGC3221; associated with McClure surname. Listed 28 February 2015.
• FGC20562 is located downstream from FGC20560 and parallel to FGC20561. Listed 17 November 2014.
• FGC20563 is located downstream from L1308. Listed 17 November 2014.
• FGC17611/Y5080 is located downstream from FGC17595/Z17612; is associated with descendants of Christopher MacRae, Constable of Eilean Donan Castle in 1511 and chief of the MacRaes of Kintail. Listed 9 October 2015.
• L150.2/PF6274.2/S351.2 was apparently found in one man immediately under L150.1, raising the possibility of a false negative without better data. Listed 17 Jan 2016.

References:

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