Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > A9507

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
22461050-C-G 20299164-C-G A11496 DYZ19 +
14069364-G-A 11948658-G-A CTS1791 YY+
2887935-C-T 3019894-C-T BY23401 YY+
7283366-A-G 7415325-A-G BY64373 YY+
8557904-C-A 8689863-C-A BY23593 YY+
8603685-C-T 8735644-C-T BY74449 YY+
8623481-G-A 8755440-G-A S11734 YY+
8982460-C-T 9144851-C-T BY23632 Y+
9796456-T-C 9958847-T-C BY81067 Y+
14065062-G-C 11944356-G-C YY+
14329117-G-T 12208411-G-T BY23816 YY+
15136230-A-G 13024317-A-G BY99875 YY+
15177268-C-A 13065354-C-A BY23881 YY+
16253123-C-G 14141243-C-G BY23943 YY+
16365134-T-C 14253254-T-C BZ2296 YY+
16544660-G-A 14432780-G-A BY23972 YY+
16852871-C-T 14740991-C-T BY23995 YY+
17031508-T-G 14919628-T-G BY24018 YY+
18065484-G-T 15953604-G-T BY24105 YY+
19115098-C-T 17003218-C-T BY24195 YY+
19120767-G-A 17008887-G-A BY24199 YY+
19218658-T-C 17106778-T-C BY24210 YY+
19218697-G-C 17106817-G-C BY24211 YY+
19222964-G-A 17111084-G-A BY24212 YY+
19450616-T-G 17338736-T-G BY24234 YY+
19486226-G-T 17374346-G-T BY24236 Y+
21715830-T-C 19553944-T-C BY24331 YY+
21861343-C-G 19699457-C-G BY135984 YY+
21936726-G-T 19774840-G-T BY136573 YY+
22478361-T-G 20316475-T-G BY24625 DYZ19 +
22561586-G-T 20399700-G-T BY24668 YY+
22718662-C-A 20556776-C-A BY24689 YY+
22917833-G-A 20755947-G-A ZS6443 YY+
23552383-G-T 21390497-G-T BY24768 YY+
23603716-G-A 21441830-G-A BY44198 YY+
23748508-C-G 21586622-C-G BY24791 Y+
24464834-T-C 22318687-T-C BY24845 Y+
26033021-C-A 23886874-C-A BY24870 P1_Y1 +
28537617-G-T 26391470-G-T BY44273 Y+
7021095-C-A 7153054-C-A **
14065060-TA-T 11944354-TA-T **
18030295-T-G 15918415-T-G BY43502 **
22219828-C-T 20057942-C-T DYZ19 **
22448840-T-G 20286954-T-G DYZ19 **
18353116-GTA-G 16241236-GTA-G P6_Prx 8×TA***
25252288-CATTATT-C 23106141-CATTATT-C P2_r1 13×ATT***
6111147-C-T 6243106-C-T ***
7495642-T-G 7627601-T-G IR1_L ***
19600316-A-G 17488436-A-G P5_Prx ***
19748172-A-T 17636292-A-T P5_Prx ***
19828646-C-T 17716766-C-T P5_Prx ***
19851457-T-A 17739577-T-A P5_Prx ***
20642500-ATATAT-A 18480614-ATATAT-A P4_Prx ***
20677033-G-A 18515147-G-A P4_Prx ***
20699061-T-C 18537175-T-C P4_Prx ***
20713312-T-C 18551426-T-C P4_Prx ***
20790978-A-G 18629092-A-G P4_Prx ***
22232708-A-T 20070822-A-T DYZ19 ***
22255028-G-A 20093142-G-A DYZ19 ***
22256011-G-C 20094125-G-C FT453721 DYZ19 ***
22259419-T-A 20097533-T-A DYZ19 ***
22272404-C-A 20110518-C-A DYZ19 ***
22285585-G-C 20123699-G-C DYZ19 ***
22285873-A-G 20123987-A-G DYZ19 ***
22285973-AG-A 20124087-AG-A DYZ19 ***
22293570-G-A 20131684-G-A BY50640 DYZ19 ***
22308201-G-T 20146315-G-T ZS11493 DYZ19 ***
22334773-G-T 20172887-G-T DYZ19 ***
22335120-G-T 20173234-G-T DYZ19 ***
22335121-G-T 20173235-G-T DYZ19 ***
22362091-T-C 20200205-T-C BY182175 DYZ19 ***
22362097-G-T 20200211-G-T BY165693 DYZ19 ***
22363957-C-A 20202071-C-A DYZ19 ***
22423450-A-C 20261564-A-C DYZ19 ***
24320532-G-A 22174385-G-A P3_t1 ***
25047851-C-G 22901704-C-G g1 ***
25051660-G-A 22905513-G-A g1 ***
25859511-A-G 23713364-A-G P1_Y1 ***
25886189-A-T 23740042-A-T P1_Y1 ***
25929561-C-A 23783414-C-A P1_Y1 ***
26179897-G-A 24033750-G-A P1_Y1 ***
26564111-A-T 24417964-A-T P1_g2 ***
13834028-TATGGA-T 11713322-TATGGA-T 7×ATGGA***
19748163-C-CT 17636283-C-CT P5_Prx 8×T***

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.