Tree Position

R-P312/S116 > Z290 > L21/S145 > DF63/S522 > CTS6919 > A92 > BY654

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	STR	FTDNA 317688	Manual Edits
15702033-AAC-A	13590153-AAC-A							+
13998700-A-G	11877994-A-G		BY92171		Y	Y		+
2790473-C-A	2922432-C-A		Y81448					***
20642083-G-C	18480197-G-C			P4_Prx				***
22487797-C-T	20325911-C-T			DYZ19				***

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:

Kit	POSITION-REF-ALT (hg19)	POSITION-REF-ALT (hg38)	Note
Manual	14592271-G-A	12480471-G-A	2A
Manual	18443360-C-A	16331480-C-A	18A
Manual	23817864-C-A	21655978-C-A	6A

Haplotype Progression

The data below reveals the progression of changes in the haplotype. The bottom row is the haplotype for this man and above him are the inferred ancestral haplotypes for various upstream blocks. These inferred haplotypes are very much a work in progress, and any suggested modifications are appreciated. I think we can use our vast collection of haplotype data to refine these haplotypes. Mutations made from each upstream block are shown in sequence. The cell color is determined by the block in which the mutation took place.

	DYS393	DYS390	DYS19	DYS391	DYS385	DYS426	DYS388	DYS439	DYS389i	DYS392	DYS389ii	DYS458	DYS459	DYS455	DYS454	DYS447	DYS437	DYS448	DYS449	DYS464	DYS460	Y-GATA-H4	YCAII	DYS456	DYS607	DYS576	DYS570	CDY	DYS442	DYS438	DYS531	DYS578	DYF395S1	DYS590	DYS537	DYS641	DYS472	DYF406S1	DYS511	DYS425	DYS413	DYS557	DYS594	DYS436	DYS490	DYS534	DYS450	DYS444	DYS481	DYS520	DYS446	DYS617	DYS568	DYS487	DYS572	DYS640	DYS492	DYS565	DYS710	DYS485	DYS632	DYS495	DYS540	DYS714	DYS716	DYS717	DYS505	DYS556	DYS549	DYS589	DYS522	DYS494	DYS533	DYS636	DYS575	DYS638	DYS462	DYS452	DYS445	Y-GATA-A10	DYS463	DYS441	Y-GGAAT-1B07	DYS525	DYS712	DYS593	DYS650	DYS532	DYS715	DYS504	DYS513	DYS561	DYS552	DYS726	DYS635	DYS587	DYS643	DYS497	DYS510	DYS434	DYS461	DYS435
P312/S116	13	24	14	11	11-14	12	12	12	13	13	29	17	9-10	11	11	25	15	19	29	15-15-17-17	11	11	19-23	16	15	18	17	36-38	12	12	11	9	15-16	8	10	10	8	10	10	12	23-23	16	10	12	12	15	8	12	22	20	13	12	11	13	11	11	12	12	33	15	9	16	12	26	26	19	12	11	13	12	10	9	12	12	10	11	11	30	12	13	24	13	10	10	20	15	19	13	24	17	12	15	24	12	23	18	10	14	17	9	12	11
L21/S145	13	24	14	11	11-14	12	12	12	13	13	29	17	9-10	11	11	25	15	19	29	15-15-17-17	11	11	19-23	16	15	18	17	36-38	12	12	11	9	15-16	8	10	10	8	10	10	12	23-23	16	10	12	12	15	8	12	22	20	13	12	11	13	11	11	12	12	35	15	9	16	12	25	26	19	12	11	13	12	11	9	12	12	10	11	11	30	12	13	24	13	10	10	20	15	19	13	24	17	12	15	24	12	23	18	10	14	17	9	12	11
DF63/S522	13	24	14	11	11-14	12	12	12	13	13	29	17	9-10	11	11	25	15	19	29	15-15-17-17	11	11	19-23	16	15	18	17	36-38	12	12	11	9	15-16	8	10	10	8	10	10	12	23-23	16	10	12	12	15	8	12	22	20	14	12	11	13	11	11	12	12	35	15	9	16	12	25	26	19	12	11	13	12	11	9	12	12	10	11	11	30	12	13	24	13	10	10	20	15	19	13	24	17	12	15	24	12	23	18	10	14	17	9	12	11
CTS6919	13	24	14	11	11-14	12	12	12	14	13	30	17	9-10	11	11	25	15	19	29	15-15-17-17	11	11	19-23	16	15	19	17	36-38	12	12	11	9	15-16	8	10	10	8	10	10	12	23-23	16	10	12	12	16	8	12	22	20	14	12	11	13	11	11	12	12	35	15	9	16	12	25	26	19	12	11	13	12	11	9	12	12	10	11	11	30	12	13	24	13	10	10	20	15	19	13	24	17	12	15	24	12	23	18	10	14	17	9	12	11
A92	13	24	14	11	11-14	12	12	12	14	13	30	17	9-10	11	11	25	15	19	29	15-15-17-17	11	11	19-23	16	15	19	17	36-38	12	12	11	9	15-16	8	10	10	8	10	10	12	23-23	16	10	12	12	16	8	12	22	20	14	12	11	13	11	11	12	12	35	15	9	16	12	25	26	19	12	11	13	12	11	9	12	12	10	11	11	30	12	13	24	13	10	10	20	15	19	13	24	17	12	15	24	12	23	18	10	14	17	9	12	11
BY654	13	24	14	11	11-14	12	12	12	14	13	30	17	9-10	11	11	25	15	19	29	15-15-17-17	11	10	19-23	16	15	19	17	36-38	12	12	11	10	15-16	8	10	10	8	11	10	12	23-23	16	10	12	12	16	8	12	22	20	14	12	11	13	11	11	12	12	33	15	9	16	12	25	26	19	12	11	12	12	8	9	12	12	10	11	11	30	12	13	24	13	10	10	20	15	17	13	23	17	12	15	24	12	23	18	10	14	17	9	12	11
Franklin	13	24	14	11	11-14	12	12	12	14	13	30	17	9-10	11	11	25	15	19	29	15-15-17-17	11	10	19-22	16	16	19	17	35-39	12	12	11	10	15-16	8	10	10	8	11	10	12	23-23	16	10	12	12	16	8	12	22	20	14	12	11	13	11	11	12	12	33	15	9	16	12	25	26	19	12	11	12	12	8	9	12	12	10	11	11	30	12	13	24	13	10	10	20	15	17	13	23	17	12	15	24	12	23	18	10	14	17	9	12	11

Age Analysis Information (work in progress)

	All	McDonald	YFull
Kit: 317688	10664208	7714048	7790934
Used in age calculations	10664208	7714048	7790934
Counts of SNPs		1	1

Variant counts last updated 2018-06-07 23:39:26.

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