Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > S14469 > S23682 > FGC4220 > FGC36253 > FGC36273

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
B182201
20869252-C-T 18707366-C-T P4_Dst A*
28816773-G-T 26670626-G-T A*
3010034-C-A 3141993-C-A A*
3237652-C-T 3369611-C-T A*
16105955-A-G 13994075-A-G P8_Prx A*
16160535-T-C 14048655-T-C P8_Dst A*
18303458-G-A 16191578-G-A P6_Prx A*
19860826-C-CA 17748946-C-CA P5_Prx 8×AA*
20869263-G-T 18707377-G-T P4_Dst A*
22312933-C-T 20151047-C-T DYZ19 A*
24208128-C-T 22061981-C-T P3_b1 A*
24670559-G-A 22524412-G-A P3_b2 A*
25942581-C-T 23796434-C-T P1_Y1 A*
26353437-C-T 24207290-C-T P1_Y1 A*
28682050-G-A 26535903-G-A CTS12721 PF4936 +
18263316-G-A 16151436-G-A CTS8886 +
23421148-C-T 21259262-C-T FT58774 YY+
21797244-C-A 19635358-C-A PF6328 YY+
2970820-T-C 3102779-T-C FT74298 +
5934551-G-T 6066510-G-T FT75443 +
3202636-C-T 3334595-C-T FT74397 +
3239657-C-T 3371616-C-T FT74412 +
3955711-A-G 4087670-A-G FT74685 +
4031655-G-A 4163614-G-A FT74720 +
4340222-T-C 4472181-T-C FT74824 +
4598170-C-T 4730129-C-T FT74924 +
5237366-G-A 5369325-G-A FT75185 +
5359335-A-G 5491294-A-G BY58673 +
5500973-A-T 5632932-A-T FT75288 +
5835677-T-A 5967636-T-A FT75408 +
5915340-C-A 6047299-C-A FT75434 +
6035036-T-G 6166995-T-G FT75485 +
6612280-C-T 6744239-C-T FT75614 +
6773537-CTTTCCTTCCTTCCTTCTTTTCTAT-C 6905496-CTTTCCTTCCTTCCTTCTTTTCTAT-C +
6865704-A-T 6997663-A-T BY61826 YY+
7822419-G-T 7954378-G-T BY67957 YY+
8308813-C-T 8440772-C-T BY71582 YY+
8745618-G-T 8877577-G-T BY75572 YY+
9722295-T-C 9884686-T-C FT76021 IR3_Prx +
9866010-T-G 10028401-T-G BY81590 YY+
9980242-G-C 10142633-G-C BY82373 Y+
10082397-G-A 10244788-G-A FT371281 +
10758472-A-G FT371282 +
13251672-A-T 11095996-A-T +
13315472-C-G 11159796-C-G FT92354 +
13530916-A-G 11375240-A-G FT444818 +
14293598-C-T 12172892-C-T FT76236 YY+
14830996-C-T 12719063-C-T FT76345 YY+
15594305-T-A 13482425-T-A BY102774 YY+
17490645-A-G 15378765-A-G BY115183 YY+
17662965-T-C 15551085-T-C BY116454 YY+
17672638-A-G 15560758-A-G BY116536 YY+
17931434-A-T 15819554-A-T FT76842 Y+
17960674-A-C 15848794-A-C BY118751 YY+
18137088-G-A 16025208-G-A BY120359 YY+
18789389-G-A 16677509-G-A BY123926 YY+
19021063-C-T 16909183-C-T BY125565 YY+
19137828-G-T 17025948-G-T FT77020 Y+
19230523-A-T 17118643-A-T BY127489 YY+
19232968-T-A 17121088-T-A BY127520 YY+
19381655-A-T 17269775-A-T BY128634 YY+
19508531-C-T 17396651-C-T BY129681 YY+
21133689-T-C 18971803-T-C BY156878 YY+
21135545-C-T 18973659-C-T BY130609 YY+
21824998-C-T 19663112-C-T BY135736 YY+
22923106-A-C 20761220-A-C BY141752 YY+
22924510-G-C 20762624-G-C BY141762 YY+
23456271-G-A 21294385-G-A BY145416 YY+
23811414-TTAC-T 21649528-TTAC-T +
24422420-G-C 22276273-G-C FT77565 Y+
21464771-G-GTTCTTCTTC 19302885-G-GTTCTTCTTC 16×TTC*
19567287-C-CAACTA 17455407-C-CAACTA 7×AACTA*
16236233-A-AAAAC 14124353-A-AAAAC 8×AAAC*
13447968-C-A 11292292-C-A *
13268619-T-A,C 11112943-T-A,C *
21623520-A-AACAC 19461634-A-AACAC 19×AC*
22234024-T-C 20072138-T-C DYZ19 *
16096802-T-C 13984922-T-C FT451986 **
19611177-G-T 17499297-G-T P5_Prx **
14761100-TGATAGATA-T 12649169-TGATAGATA-T 12×GATA**
17957-A-G **
19696433-TAAA-T 17584553-TAAA-T P5_Prx 14×A**
18322899-T-C 16211019-T-C P6_Prx **
20620877-C-A 18458991-C-A P4_Prx **
23720041-C-A 21558155-C-A **
14445402-G-A 12324675-G-A FTA21788 **
16096812-A-C 13984932-A-C **
26324270-GTT-G 24178123-GTT-G P1_Y1 20×T**
5520717-T-C 5652676-T-C FT370393 **
6240907-ATT-A 6372866-ATT-A IR3_Dst 12×T**
9471179-G-A 9633570-G-A BY79663 **
19709446-A-G 17597566-A-G P5_Prx **
20050792-T-G 17938912-T-G P5_Prx **
24333113-T-G 22186966-T-G P3_t1 **
25915687-C-A 23769540-C-A P1_Y1 **
7414277-CAA-C 7546236-CAA-C 27×A***
13846224-T-TGAATG 11725518-T-TGAATG 11×GAATG***
24290683-TA-T,TAA 22144536-TA-T,TAA P3_t1 11×A***
10908423-G-A ***
3403261-CAAAA-C 3535220-CAAAA-C 30×A***
10973831-T-C ***
13571665-AT-A,ATT 11415989-AT-A,ATT 17×T***
28686423-CAAA-C,CAA 26540276-CAAA-C,CAA 21×A***
14850653-T-G 12738719-T-G ***
16904731-AGTGTGTGTGTGTGT-A 14792851-AGTGTGTGTGTGTGT-A 20×GT***
19146569-CTTTTTTTT-C,CTTT 17034689-CTTTTTTTT-C,CTTT 28×T***
21394422-C-T 19232536-C-T ***
21394479-T-C 19232593-T-C ***

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.