Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z198 > Z46513 > ZS312 > Z262 > BY32601

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
28732282-T-A 26586135-T-A M6346 BY42690M6346 Y8×A+
6154329-T-C 6286288-T-C BY59350 IR3_Dst +
6461215-A-C 6593174-A-C BY60252 +
7203558-A-C 7335517-A-C BY63864 YY+
7636294-C-T 7768253-C-T BY66425 YY+
7717046-G-A 7849005-G-A BY67094 YY+
7736480-A-G 7868439-A-G BY67221 YY+
7937302-C-T 8069261-C-T BY68891 YY+
7962706-T-C 8094665-T-C BY69095 YY+
8021660-C-A 8153619-C-A BY69418 YY+
8313810-G-A 8445769-G-A FGC14238 Y5997 YY+
8422066-G-A 8554025-G-A BY72574 YY+
8771256-G-A 8903215-G-A BY75768 YY+
9404146-G-A 9566537-G-A BY79250 YY+
13651644-A-G 11495968-A-G BY87089 +
14101902-T-C 11981196-T-C BY32615 YY+
14169389-C-T 12048683-C-T BY82274Y130371 YY+
14241310-C-T 12120604-C-T BY94224 YY+
15981102-A-G 13869222-A-G BY105291 YY+
16413941-C-T 14302061-C-T BY107623 YY+
16494678-C-T 14382798-C-T BY108196 YY+
17444191-C-T 15332311-C-T BY114854 YY+
17832699-C-T 15720819-C-T BY117688 YY+
17892022-G-T 15780142-G-T BY118180 YY+
18171052-G-A 16059172-G-A BY120591 YY+
19045828-G-T 16933948-G-T BY125751 YY+
19066562-C-T 16954682-C-T BY55145 YY+
21204863-G-C 19042977-G-C BY131082 YY+
21434468-G-T 19272582-G-T BY132890 YY+
21549552-A-G 19387666-A-G BY133745 YY+
21982247-A-G 19820361-A-G BY136834 YY+
22180589-A-G 20018703-A-G BY138216 YY+
22466764-G-T 20304878-G-T BY52948 DYZ19 +
22476046-C-A 20314160-C-A BY223504 DYZ19 +
22554322-G-A 20392436-G-A BY55364 YY+
22645675-A-G 20483789-A-G BY139704 YY+
22831351-T-C 20669465-T-C BY141122 YY+
23823660-C-T 21661774-C-T BY148067 Y+
28307183-T-C 26161036-T-C P1_b4 +
13699420-C-A 11543744-C-A **
15183873-C-A 13071959-C-A CTS3793 **
13705888-G-C 11550212-G-C ***
13710601-A-G 11554925-A-G ***
13710645-T-C 11554969-T-C ***
13715219-C-T 11559543-C-T ***
9980142-C-A 10142533-C-A ***
13705060-T-C 11549384-T-C ***
22359384-G-C 20197498-G-C DYZ19 ***
22489515-T-G 20327629-T-G DYZ19 ***
13706407-T-C 11550731-T-C BY1008 ***
13711592-T-A 11555916-T-A ***
13714619-T-A 11558943-T-A ***
18345943-AATAC-A 16234063-AATAC-A P6_Prx 9×ATAC***
22506502-T-A 20344616-T-A DYZ19 ***
22511324-C-G 20349438-C-G DYZ19 ***
13714917-G-C 11559241-G-C ***
19134848-G-GTGT 17022968-G-GTGT Z2118 12×TGT***
10017921-A-G 10180312-A-G ***
10017939-C-T 10180330-C-T ***
13715153-A-C 11559477-A-C ***
22454549-T-G 20292663-T-G DYZ19 ***
13713542-G-A,T 11557866-G-A,T ***
13724244-C-T 11568568-C-T ***
22359440-C-G 20197554-C-G DYZ19 ***
6269214-C-T 6401173-C-T IR3_Dst ***
6334793-T-A 6466752-T-A IR3_Dst ***
7447094-C-T 7579053-C-T IR1_L ***
13478121-A-C 11322445-A-C BY85988 ***
13700958-T-G 11545282-T-G 5×GAATG***
13705110-T-A 11549434-T-A ***
13711106-A-C 11555430-A-C ***
13720251-A-T 11564575-A-T ***
19688972-C-T 17577092-C-T P5_Prx ***
19818341-G-A 17706461-G-A BY3840 P5_Prx ***
19979690-T-C 17867810-T-C P5_Prx ***
20740652-C-A 18578766-C-A P4_Prx ***
20771472-A-G 18609586-A-G P4_Prx ***
20931852-CAT-C 18769966-CAT-C P4_Dst ***
22233184-C-A 20071298-C-A DYZ19 ***
22233187-T-A 20071301-T-A DYZ19 ***
22233190-T-A 20071304-T-A DYZ19 ***
22233191-A-G 20071305-A-G FGC23832 DYZ19 ***
22233387-A-C 20071501-A-C DYZ19 ***
22233399-T-C 20071513-T-C Y108795 DYZ19 ***
22233408-C-T 20071522-C-T DYZ19 ***
22233419-A-C 20071533-A-C DYZ19 ***
22241192-T-A 20079306-T-A DYZ19 ***
22246925-T-C 20085039-T-C DYZ19 ***
22248801-G-A 20086915-G-A DYZ19 ***
22285327-G-T 20123441-G-T DYZ19 ***
22340074-A-G 20178188-A-G DYZ19 ***
22447981-A-T 20286095-A-T DYZ19 ***
25028028-G-A 22881881-G-A g1 ***
25154573-T-C 23008426-T-C g1 ***
25169028-A-G 23022881-A-G g1 ***
25277078-ATTAT-A 23130931-ATTAT-A P2_r1 ***
25283400-C-T 23137253-C-T P2_r1 ***
25388623-A-G 23242476-A-G P2_r2 ***
25887991-T-C 23741844-T-C P1_Y1 ***
26162123-G-C 24015976-G-C P1_Y1 ***

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.