Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Z251/S470 > S11556 > S9294 > BY3229 > BY3231 > BY43237 > FGC11986 > BY9004 > BY9006

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
22440849-A-G 20278963-A-G PF1856 DYZ19 +
22440497-T-G 20278611-T-G A4268 DYZ19 +
2880239-T-C 3012198-T-C Y81691 YY+
6841305-C-T 6973264-C-T Y82661 YY+
7313819-C-T 7445778-C-T Y83876 YY+
7650982-T-C 7782941-T-C Y84571 YY+
7715171-C-A 7847130-C-A Y84746 YY+
7762362-T-A 7894321-T-A Y84885 YY+
8054798-C-A 8186757-C-A Y85728 YY+
8199569-C-A 8331528-C-A Y86074 YY+
8508817-C-T 8640776-C-T Y87137 YY+
8846256-G-A 8978215-G-A Y88163 YY+
9381451-C-G 9543842-C-G Y88838 Y+
13693887-C-T 11538211-C-T BY88818 +
14248156-G-A 12127450-G-A Y90809 YY+
14777301-G-A 12665370-G-A Y92167 YY+
15386916-G-A 13275036-G-A Y93676 YY+
15481251-ATATT-A 13369371-ATATT-A +
16297956-CAGAT-C 14186076-CAGAT-C +
17320505-T-C 15208625-T-C Y98775 YY+
17443430-T-C 15331550-T-C Y99170 YY+
17550434-C-G 15438554-C-G Y99502 YY+
18197447-A-G 16085567-A-G Y101603 YY+
18612170-T-C 16500290-T-C Y102224 YY+
18661120-TC-T 16549240-TC-T +
19351232-A-G 17239352-A-G Y104474 YY+
19395442-G-A 17283562-G-A Y104604 YY+
22072455-G-C 19910569-G-C Y108306 YY+
22440457-A-G 20278571-A-G BY22971 DYZ19 +
22440488-A-T 20278602-A-T BY155272 DYZ19 +
22468733-T-A 20306847-T-A BY52980 DYZ19 +
22485450-G-T 20323564-G-T Z34323 DYZ19 +
22753767-G-A 20591881-G-A Y109657 YY+
22797437-T-C 20635551-T-C Y109782 YY+
23746850-C-T 21584964-C-T BY147333 Y+
23752091-C-G 21590205-C-G Y112225 Y+
24395118-C-T 22248971-C-T Y112744 Y+
21476880-C-A 19314994-C-A **
13971476-G-A 11850770-G-A PF639 **
13418530-A-T 11262854-A-T **
17520111-G-A 15408231-G-A **
19375658-G-GCCC 17263778-G-GCCC **
22440475-G-A 20278589-G-A A4266 DYZ19 **
22440477-A-T 20278591-A-T A4267 DYZ19 **
26995874-G-A 24849727-G-A P1_r4 **
4841680-G-A 4973639-G-A Z448 FGC3353 ***
9344827-C-T 9507218-C-T ***
9320508-C-T 9482899-C-T ***
19676218-T-C 17564338-T-C P5_Prx ***
19905412-G-A 17793532-G-A P5_Prx ***
22239088-G-T 20077202-G-T BY213889 DYZ19 ***
22248803-T-A 20086917-T-A DYZ19 ***
22257588-T-A 20095702-T-A BY25033 DYZ19 ***
22270182-C-T 20108296-C-T BY214943 DYZ19 ***
22284566-G-A 20122680-G-A DYZ19 ***
22292032-T-C 20130146-T-C DYZ19 ***
22433692-T-A 20271806-T-A DYZ19 ***
22435469-T-C 20273583-T-C DYZ19 ***
22442297-T-G 20280411-T-G DYZ19 ***
22442309-C-A 20280423-C-A BY158451 DYZ19 ***
22457558-G-C 20295672-G-C FT457141 DYZ19 ***
22481294-G-T 20319408-G-T DYZ19 ***
24252085-T-C 22105938-T-C P3_b1 ***
24258461-C-G 22112314-C-G P3_b1 ***
24979269-C-T 22833122-C-T g1 ***
25064515-A-G 22918368-A-G g1 ***
25084931-C-T 22938784-C-T g1 ***
25152885-G-A 23006738-G-A g1 ***
25190440-T-C 23044293-T-C g1 ***
25717193-A-C 23571046-A-C P1_b3 ***
25980000-A-G 23833853-A-G P1_Y1 ***
26125921-CTGGA-C 23979774-CTGGA-C P1_Y1 ***
26183168-T-C 24037021-T-C P1_Y1 ***
27684407-A-C 25538260-A-C P1_Y2 ***
28792202-G-A 26646055-G-A ***
6129176-CTTT-C 6261135-CTTT-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.