Tree Position

R-U106/S21 > Z2265 > Z381/S263 > Z301/S499 > L48 > CTS3104 > A290 > S6941 > Exact position not yet finalized.

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
B327467
25889836-G-GTAA 23743689-G-GTAA P1_Y1 9×TAAA*
18275616-C-T 16163736-C-T P6_Prx A*
18357740-A-G 16245860-A-G P6_Prx A*
19785072-G-T 17673192-G-T P5_Prx A*
25578647-T-C 23432500-T-C P1_gr1 A*
25880178-C-T 23734031-C-T P1_Y1 A*
25962923-A-G 23816776-A-G P1_Y1 A*
26316582-C-A 24170435-C-A P1_Y1 A*
26337255-C-A 24191108-C-A P1_Y1 A*
26504812-T-A 24358665-T-A P1_Y1 A*
56833620-C-G A*
56834005-C-T A*
18943495-T-A 16831615-T-A L96PF2542 YY+
4676867-T-TA 4808826-T-TA 9×A+
23750776-G-A 21588890-G-A Y128521 Y+
2995638-A-T 3127597-A-T FT58926 +
7171018-A-G 7302977-A-G FT59172 YY+
8615335-G-A 8747294-G-A FT59226 YY+
8725742-G-C 8857701-G-C FT59232 YY+
13453862-C-A 11298186-C-A +
14064140-C-T 11943434-C-T FT59290 YY+
14079429-A-G 11958723-A-G FT59291 YY+
14336791-C-T 12216086-C-T FT59303 YY+
14432822-G-A 12312095-G-A FT59311 Y+
14580547-A-G 12468747-A-G FT59323 YY+
14679620-G-A 12567686-G-A FT59328 Y+
14711767-C-G 12599834-C-G FT59329 YY+
14735399-G-A 12623467-G-A FT59333 YY+
14746534-C-A 12634603-C-A FT59335 YY+
14746883-G-C 12634952-G-C FT59336 YY+
15085634-G-A 12973724-G-A FT59345 YY+
15338614-T-C 13226732-T-C FT59357 YY+
15558471-T-C 13446591-T-C YY+
15726043-C-A 13614163-C-A FT59382 YY+
15943280-G-A 13831400-G-A FT59389 Y+
16433381-T-C 14321501-T-C FT59420 YY+
16491813-G-A 14379933-G-A FT59424 YY+
16565675-G-A 14453795-G-A FT59429 YY+
17255722-G-A 15143842-G-A FT59458 YY+
18003591-G-A 15891711-G-A FT59506 P7_Gap Y+
18596645-C-T 16484765-C-T FT59523 YY+
21283544-G-T 19121658-G-T FT59585 YY+
21362188-GT-G 19200302-GT-G +
21532180-A-G 19370294-A-G FT59598 YY+
21710304-ACTT-A 19548418-ACTT-A +
21922273-C-T 19760387-C-T FT59613 YY+
22126954-A-C 19965068-A-C FT59619 YY+
22174344-G-A 20012458-G-A FT59620 YY+
22464992-G-C 20303106-G-C FT268537 DYZ19 +
22934974-C-A 20773088-C-A FT59639 YY+
23112147-G-A 20950261-G-A FT59653 YY+
56822904-C-A +
13455231-T-TTTCCA 11299555-T-TTTCCA 5×TTCCA*
10898384-A-T *
22233444-A-C 20071558-A-C DYZ19 *
18944373-AAAAAC-A 16832493-AAAAAC-A 7×AAAAC**
15993683-A-G 13881803-A-G BY12313BY12338 **
3463851-C-CAA 3595810-C-CAA 18×A**
26383340-CTT-C 24237193-CTT-C P1_Y1 16×T**
22970055-C-T 20808169-C-T FT262336 **
28565722-TTATA-T 26419575-TTATA-T 13×TA**
4305759-T-C 4437718-T-C **
5315379-T-C 5447338-T-C **
5795856-G-T 5927815-G-T **
6623161-T-C 6755120-T-C **
13207303-C-T 11051627-C-T **
13494858-A-AT 11339182-A-AT **
16885295-A-G 14773415-A-G **
17012743-C-T 14900863-C-T **
17988595-T-A 15876715-T-A P7_Prx **
17991422-A-G 15879542-A-G FTB39462 P7_Prx **
18465352-C-A 16353472-C-A P6_Dst **
21789885-T-C 19627999-T-C **
22989770-TC-T 20827884-TC-T **
26219072-A-G 24072925-A-G P1_Y1 **
28086240-A-G 25940093-A-G P1_Y2 **
28622110-G-A 26475963-G-A **
4472639-C-T 4604598-C-T ***
24387986-CTA-C 22241839-CTA-C ***
2805529-CAAAAAAA-C 2937488-CAAAAAAA-C 22×A***
16409013-CTTT-C,CT 14297133-CTTT-C,CT 18×T***
17664754-G-C 15552874-G-C ***
3812700-G-GA 3944659-G-GA 9×A***
3522968-TAAA-T,TAA 3654927-TAAA-T,TAA 24×A***
4401366-A-G 4533325-A-G ***
4878246-CAAA-C,CAA 5010205-CAAA-C,CAA 18×A***
5609585-A-AT 5741544-A-AT ***
6642706-T-C 6774665-T-C ***
6739976-G-T 6871935-G-T ***
14236042-AG-A,G 12115336-AG-A,G ***
16305924-C-CAAA 14194044-C-CAAA 24×A***
17770173-G-A 15658293-G-A ***
21095919-T-C 18934033-T-C ***
21386602-TG-T 19224716-TG-T ***
22623126-G-T 20461240-G-T ***
23823666-T-C 21661780-T-C ***
26723558-T-C 24577411-T-C P1_g2 ***
28498866-TAA-T,TA 26352719-TAA-T,TA 13×A***

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.