Tree Position

R-P312/S116 > DF19/S232 > Z302/S233 > FT11655 > Z8193 > BY3448

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 STR1kG
13847208-C-G 11726502-C-G +
21938654-T-C 19776768-T-C BY3227BY24346 YY+
22457290-G-C 20295404-G-C DYZ19 +
7642779-A-T 7774738-A-T V1317 YY+
7768494-A-G 7900453-A-G V1416 YY+
7860154-G-C 7992113-G-C FT300264 YY+
8689377-C-T 8821336-C-T V2462 YY+
8755750-A-G 8887709-A-G FT300529 YY+
9012982-C-T 9175373-C-T FT300598 Y+
9888980-G-A 10051371-G-A FT300685 Y+
14571401-T-C 12459601-T-C FT300970 YY+
14959237-C-G 12847312-C-G S3611 V2717 YY+
16435146-C-T 14323266-C-T S4325 YY+
16470941-C-T 14359061-C-T S3613 CTS5761 Y+
16974620-C-A 14862740-C-A Y+
17028253-C-T 14916373-C-T S3617 YY+
17163448-A-G 15051568-A-G Y+
17418042-C-T 15306162-C-T S3620 YY+
17418470-C-T 15306590-C-T CTS7321 S3621 YY+
18192949-C-T 16081069-C-T FT301867 YY+
18740765-C-T 16628885-C-T S3623 V3459 YY+
19145056-A-C 17033176-A-C CTS9916 S3626 V3823 YY+
19431990-A-C 17320110-A-C V4117 YY+
21065133-A-C 18903247-A-C S4333 YY+
22128949-G-T 19967063-G-T Y+
22880378-C-T 20718492-C-T FT302748 Y+
23010121-C-T 20848235-C-T FT302771 YY+
28643094-T-C 26496947-T-C FT349257 +
2956073-T-G 3088032-T-G +
2977426-C-A 3109385-C-A FT315605 +
3444239-G-C 3576198-G-C +
4203976-G-A 4335935-G-A FT319884 +
4304450-G-A 4436409-G-A +
4471078-G-T 4603037-G-T +
4908482-C-A 5040441-C-A FT322102 +
5962149-T-TATAC 6094108-T-TATAC +
5966764-A-C 6098723-A-C FT325634 +
5999764-A-G 6131723-A-G +
6085250-C-G 6217209-C-G FT326095 +
6401812-C-T 6533771-C-T +
6529731-C-T 6661690-C-T FT326827 +
6674464-TA-T 6806423-TA-T +
7590732-T-G 7722691-T-G YY+
8101347-A-G 8233306-A-G V1620 YY+
8805308-A-C 8937267-A-C YY+
13245497-T-C 11089821-T-C +
13402151-A-G 11246475-A-G +
13431684-G-T 11276008-G-T +
13462985-G-T 11307309-G-T FTB62565 +
13622526-C-T 11466850-C-T +
13634487-G-C 11478811-G-C +
13681524-G-A 11525848-G-A FTB62566 +
13843031-G-T 11722325-G-T FT328671 +
13852020-TG-T 11731314-TG-T +
14316200-TG-T 12195494-TG-T +
14610689-CCA-C 12498891-CCA-C +
14625227-TAAATAC-T 12513427-TAAATAC-T +
16842081-A-G 14730201-A-G CTS6356 YY+
17433915-C-T 15322035-C-T CTS7350 Y+
18283957-G-T 16172077-G-T P6_Prx +
18978841-G-A 16866961-G-A FT302031 YY+
19029207-A-G 16917327-A-G Y+
21707710-A-G 19545824-A-G S4313 YY+
22243854-G-A 20081968-G-A DYZ19 +
22464702-T-A 20302816-T-A DYZ19 +
22489166-G-T 20327280-G-T DYZ19 +
22851474-C-A 20689588-C-A S3634 YY+
22864052-G-A 20702166-G-A YY+
23757992-A-C 21596106-A-C Y+
25200909-G-A 23054762-G-A g1 +
26344858-C-T 24198711-C-T P1_Y1 +
28461721-TC-T 26315574-TC-T +
28529269-C-T 26383122-C-T +
28534958-TGC-T 26388811-TGC-T +
28779596-T-A 26633449-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.

Mutation Notes:

Manual13840815-C-CGAATG11720109-C-CGAATGThe reference sequence has 9 repeats of GAATG. The data has just 3 reads aligned properly and in a suitable position to cover the whole sequence. They all show the insertion.
Manual24083207-G-A21937060-G-A1 A read, and 2 G reads.
Manual18031963-GAGGA-G15920083-GAGGA-GThere really isn't any coverage here.
Manual6292510-A-G6424469-A-G2A 1G
Manual22231658-G-T20069772-G-T2G 6T
Manual22232780-G-T20070894-G-T2G 6T
Manual25247111-G-T23100964-G-T2G 6T
Manual18009932-A-C15898052-A-C2C 1A. The read with 1A has other mismatches.
Manual26395948-G-A24249801-G-A2G 1A