Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > S1026 > BY173538

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STRBigY3
B442478
25610040-A-G 23463893-A-G P1_gr1 A+
23896778-G-C 21734892-G-C YA+
23896577-G-C 21734691-G-C YA+
20132312-C-T 18020432-C-T P5_Dst A+
28817764-A-T 26671617-A-T A*
13687374-A-G 11531698-A-G A*
18355998-A-G 16244118-A-G P6_Prx A*
13687326-G-T 11531650-G-T A*
19674806-G-T 17562926-G-T P5_Prx A*
19772851-T-C 17660971-T-C P5_Prx A*
19925206-A-G 17813326-A-G P5_Prx A*
19940433-C-T 17828553-C-T P5_Prx A*
20721362-C-G 18559476-C-G P4_Prx A*
19631730-T-G 17519850-T-G P5_Prx A*
13687328-A-G 11531652-A-G A*
26380166-T-C 24234019-T-C P1_Y1 A*
28816647-C-T 26670500-C-T A*
25932232-C-A 23786085-C-A P1_Y1 A*
22313090-T-G 20151204-T-G DYZ19 A*
13825790-A-T 11705084-A-T FT67541 +
14238658-G-A 12117952-G-A FT67683 YY+
14255394-G-A 12134688-G-A FT67686 Y+
14783568-C-T 12671638-C-T BY97582 YY+
16199087-TG-T 14087207-TG-T +
14790676-G-C 12678747-G-C FT67813 YY+
14859353-C-G 12747419-C-G FT67827 YY+
14926189-C-T 12814254-C-T FT67836 YY+
15138201-T-C 13026288-T-C FT67859 YY+
11648755-G-A FT219183 +
15350217-C-G 13238336-C-G FT67890 YY+
15350240-C-A 13238359-C-A FT67891 YY+
22138544-C-T 19976658-C-T BY176042 YY+
16886832-C-T 14774952-C-T FT68178 YY+
16950632-C-T 14838752-C-T FT68194 YY+
21143776-C-T 18981890-C-T FT68740 YY+
17809896-A-T 15698016-A-T FT68382 YY+
18588557-C-G 16476677-C-G FT68510 YY+
18715842-T-C 16603962-T-C FT68542 YY+
19053308-A-G 16941428-A-G FT68602 YY+
19064532-A-G 16952652-A-G FT5949 Y+
24427436-G-T 22281289-G-T FT69282 Y+
23839634-A-C 21677748-A-C FT69246 Y+
23582334-T-C 21420448-T-C FT69201 YY+
19997455-G-A 17885575-G-A P5_Prx +
23200485-T-C 21038599-T-C FT69128 Y+
17630952-C-G 15519072-C-G FT68346 YY+
14160188-C-A 12039482-C-A FGC10413 Y+
3894561-G-T 4026520-G-T FT66294 +
6848909-G-A 6980868-G-A FGC52530 YY+
2809498-T-C 2941457-T-C FT66009 YY+
3240353-A-G 3372312-A-G FT66102 +
3836795-G-A 3968754-G-A FT66280 +
3846757-C-T 3978716-C-T FT66284 +
4049237-C-G 4181196-C-G FT66337 +
4049247-A-G 4181206-A-G FT66338 +
4186648-C-A 4318607-C-A FT66383 +
4762461-T-C 4894420-T-C FT66531 +
6402432-G-A 6534391-G-A FT66912 +
18022998-C-CA 15911118-C-CA +
5161359-C-T 5293318-C-T FT66644 +
7955841-G-A 8087800-G-A FT67217 YY+
10665290-C-T FT219184 +
8669778-T-C 8801737-T-C FT67382 YY+
8738177-C-T 8870136-C-T FT67400 YY+
10057192-C-T 10219583-C-T FT219185 +
9108458-T-C *
22237854-C-T 20075968-C-T DYZ19 *
19138110-C-CTA 17026230-C-CTA 9×TA**
10810638-T-G **
56828304-C-G **
4986102-A-G 5118061-A-G FT17064 **
14938128-G-A 12826203-G-A **
27572553-T-TTC 25426406-T-TTC P1_Y2 **
9482556-G-A 9644947-G-A **
2668201-A-T 2800160-A-T **
22622301-A-G 20460415-A-G **
19565645-A-G 17453765-A-G FT102781 **
3577550-A-G 3709509-A-G ***
22256219-T-C 20094333-T-C FT219186 DYZ19 ***
28522376-CTTTT-C,CTTT 26376229-CTTTT-C,CTTT 18×T***
8218067-TTCTT-T,TTCTC 8350026-TTCTT-T,TTCTC ***
22320081-G-T 20158195-G-T DYZ19 ***
2840099-CAAAAAAAAA-C 2972058-CAAAAAAAAA-C 20×A***
27481929-CT-C 25335782-CT-C P1_Y2 9×T***
10020526-G-C 10182917-G-C ***
28785994-T-A 26639847-T-A ***
13484458-T-A 11328782-T-A ***
22441416-T-A 20279530-T-A DYZ19 ***
13464525-T-A,G 11308849-T-A,G ***
21417102-T-C 19255216-T-C ***
16494370-TGTAG-T 14382490-TGTAG-T ***
13464537-C-G 11308861-C-G ***
13292244-T-G 11136568-T-G ***
14565234-A-T 12453434-A-T ***
12807338-CTTTTTTTTTTTTTTTTTTTTTTTT-C,CTTTTT 43×T***
7717681-TTTCT-T,TTTCC 7849640-TTTCT-T,TTTCC ***
6714066-T-C 6846025-T-C ***
15839959-T-TAA 13728079-T-TAA 17×A***
5129835-T-C 5261794-T-C ***
17951299-ATT-A,ATTT 15839419-ATT-A,ATTT 25×T***
4983174-ATT-A,AT 5115133-ATT-A,AT 28×T***
18539230-C-T 16427350-C-T ***
3999821-GTA-G,GTATATATA 4131780-GTA-G,GTATATATA 17×TA***
13464534-T-A 11308858-T-A ***
3809136-ATTTTTTTTTT-A 3941095-ATTTTTTTTTT-A 31×T***
3220615-C-A 3352574-C-A ***
13464545-C-A 11308869-C-A ***
19138549-C-CTA 17026669-C-CTA ***

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: B4424781500892994203358335718
Used in age calculations1500892994203358335718
Counts of SNPs2727
Variant counts last updated 2020-03-16 02:55:20.



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