Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > Z295/S1217 > S25783 > CTS4065 > FGC34881

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 STRFTDNA
3472928-C-T 3604887-C-T A+
25560670-G-A 23414523-G-A BY23451 P1_gr1 ***A*
59004482-A-G 56858335-A-G A*
21022787-G-GA 18860901-G-GA P4_Dst 11×AA*
26015650-A-G 23869503-A-G P1_Y1 ***A*
20081567-T-TA 17969687-T-TA P5_Dst 10×AA*
20974872-G-GCAA 18812986-G-GCAA P4_Dst 11×CAAA*
56837114-G-A A*
19574674-T-C 17462794-T-C P5_Prx YA*
24296165-G-C 22150018-G-C P3_t1 A*
16020409-T-G 13908529-T-G L530 YY++
16196343-G-A 14084463-G-A BY43426 YY++
14789575-C-T 12677646-C-T BY56510FGC60444 Y29933 YY+
7646321-C-T 7778280-C-T Y84558 YY++
8271124-TC-T 8403083-TC-T ++
8319836-A-G 8451795-A-G Y86469 YY++
8721551-A-G 8853510-A-G Y87819 YY++
14265261-A-T 12144555-A-T ZS8229 YY++
14654608-G-A 12542673-G-A Y91907 YY++
15038812-G-A 12926902-G-A Y92863 YY++
15497185-C-T 13385305-C-T Y93939 Y**+
16185084-A-G 14073204-A-G Y95545 Y++
16580749-C-G 14468869-C-G Y96757 YY++
18004024-C-T 15892144-C-T Y100912 P7_Gap Y++
18414333-C-T 16302453-C-T Y101949 P6_Gap ++
18753146-A-T 16641266-A-T Y102591 YY++
18808625-C-A 16696745-C-A Y102732 YY++
19023526-G-A 16911646-G-A FGC3088 YY++
19409569-C-T 17297689-C-T BY128863 YY++
21311767-A-G 19149881-A-G Y106092 YY++
21512600-C-A 19350714-C-A Y106729 YY++
21607962-T-C 19446076-T-C BY134137 YY++
21621111-C-T 19459225-C-T Y107049 YY++
22091953-G-A 19930067-G-A Y108357 YY++
22158195-G-T 19996309-G-T Y108535 YY++
23158782-T-C 20996896-T-C Y110857 Y++
24444995-A-T 22298848-A-T Y112864 Y++
6485097-C-A 6617056-C-A FT80687 +
3137673-A-C 3269632-A-C FT80330 +
3701131-A-G 3833090-A-G FT80386 +
4436899-T-G 4568858-T-G FT80467 +
4449160-A-G 4581119-A-G FT80470 +
4678896-G-A 4810855-G-A FT80498 +
5236170-T-C 5368129-T-C FT80563 +
5275909-C-T 5407868-C-T FT232861 +
5525003-A-G 5656962-A-G FT80602 +
5915498-G-A 6047457-G-A +
10071508-A-G 10233899-A-G +
10780493-C-A FT430904 +
10958512-A-G FT438197 +
13498137-T-A 11342461-T-A +
13994522-C-A 11873816-C-A FT80791 Y+
14050401-A-G 11929695-A-G FT80798 Y+
17215656-G-A 15103776-G-A FT80891 Y+
18059971-T-C 15948091-T-C YY+
19245987-C-T 17134107-C-T FT80954 YY+
21351444-A-C 19189558-A-C FT80975 Y+
21922902-G-T 19761016-G-T FT81001 YY+
17793822-A-ATATCTATC 15681942-A-ATATCTATC 11×TATC****
21216758-A-G 19054872-A-G YY****
22264709-C-T 20102823-C-T DYZ19 ****
5434604-C-T 5566563-C-T *
18414434-G-T 16302554-G-T P6_Gap *
18414438-G-T 16302558-G-T P6_Gap *
28819333-T-G 26673186-T-G **
3394403-G-C 3526362-G-C FGC34855 **
13713600-C-A 11557924-C-A BY89541 *****
27837978-GTTT-G 25691831-GTTT-G P1_Y2 29×T**
4347909-G-A 4479868-G-A **
5357500-T-TTA 5489459-T-TTA **
7852496-G-A 7984455-G-A **
13342275-G-A 11186599-G-A **
19771983-G-T 17660103-G-T P5_Prx **
20766326-A-AAT 18604440-A-AAT P4_Prx **
22235937-A-G 20074051-A-G DYZ19 **
56887009-A-G **
22455851-A-AC 20293965-A-AC DYZ19 ***
22475450-C-G 20313564-C-G DYZ19 ***
13294509-GTT-G 11138833-GTT-G 12×T***
13487968-A-C,T 11332292-A-C,T ***
22454860-G-T 20292974-G-T DYZ19 ***
14636290-G-A 12524359-G-A PR5186 Y49728 ***
22446670-G-C 20284784-G-C DYZ19 ***
13452447-C-T 11296771-C-T ***
13480755-A-G 11325079-A-G ***
25393687-A-C 23247540-A-C P2_r2 ***
59007919-C-T 56861772-C-T ***
13463412-C-T 11307736-C-T ***
14609556-C-T 12497758-C-T ***
22295937-C-T 20134051-C-T DYZ19 ***
58873305-C-T 56717566-G-A ***
13463407-C-T 11307731-C-T ***
22508059-T-A 20346173-T-A DYZ19 ***
22455823-C-G 20293937-C-G DYZ19 ***
13140531-T-A 10630017-T-A ***
58990249-T-C 56844102-T-C ***
22455856-G-C 20293970-G-C DYZ19 ***
4561212-C-A 4693171-C-A ***
6211263-C-T 6343222-C-T IR3_Dst ***
9994582-G-C 10156973-G-C ***
9994585-A-C 10156976-A-C ***
9994643-A-T 10157034-A-T ***
13462744-C-A 11307068-C-A ***
17238338-G-A 15126458-G-A FT122189 ***
19040919-G-C 16929039-G-C PR2958 ***
19993980-C-CA 17882100-C-CA P5_Prx ***
22242478-A-C 20080592-A-C DYZ19 ***
22243519-C-A 20081633-C-A DYZ19 ***
22269434-A-C 20107548-A-C DYZ19 ***
22353465-A-C 20191579-A-C DYZ19 ***
24164721-C-T 22018574-C-T P3_b1 ***
25041475-C-T 22895328-C-T g1 ***
25120511-G-A 22974364-G-A g1 ***
25281635-G-C 23135488-G-C P2_r1 ***
25394040-G-C 23247893-G-C P2_r2 ***
25394218-G-T 23248071-G-T P2_r2 ***
25825071-A-AT 23678924-A-AT P1_b3 ***
26196026-C-CA 24049879-C-CA P1_Y1 ***
26954139-T-C 24807992-T-C BY2501 P1_r3 ***
15363874-A-C 13251994-A-C ***
13488541-G-C 11332865-G-C ***
4338463-C-CTT 4470422-C-CTT 12×T***
18035665-CTTTTT-C 15923785-CTTTTT-C 30×T***
8314146-CTTTTT-C,CTTT 8446105-CTTTTT-C,CTTT 24×T***
3571667-A-G 3703626-A-G ***
13628027-C-CTATA 11472351-C-CTATA ***
22066299-T-A 19904413-T-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.