Big Tree: Person Data

Tree Position

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	1kG HG01953
20995546-TCTTTC-T	18833660-TCTTTC-T			P4_Dst			11×CTTTC	+
3570961-C-A	3702920-C-A							+
58894781-G-A	56696090-C-T							+
19346429-T-TCTTC	17234549-T-TCTTC							+
2748998-T-C	2880957-T-C		FT333398		Y	Y		+
2861387-T-C	2993346-T-C		FT333453		Y	Y		+
7560871-C-G	7692830-C-G		FT333909		Y	Y		+
7750725-C-T	7882684-C-T		FT334026		Y	Y		+
7788558-T-C	7920517-T-C		FT334051		Y	Y		+
8424426-A-C	8556385-A-C		FT334463		Y	Y		+
8589495-A-G	8721454-A-G		Z13358		Y	Y		+
8863138-G-A	8995097-G-A		FT334777		Y	Y		+
15002075-C-A	12890160-C-A		FT335899		Y	Y		+
15942628-T-C	13830748-T-C		FT336483		Y	Y		+
16037283-T-C	13925403-T-C		FT336560		Y	Y		+
16486492-G-T	14374612-G-T		FT336839		Y	Y		+
16549164-A-T	14437284-A-T		FT336884		Y	Y		+
16767285-C-T	14655405-C-T		FT337021		Y	Y		+
16999901-C-T	14888021-C-T		FT337156		Y			+
17390622-T-C	15278742-T-C		FT337406		Y	Y		+
17519156-G-C	15407276-G-C		FT337494		Y			+
17939965-T-A	15828085-T-A		FT337791		Y	Y		+
19080228-T-C	16968348-T-C				Y	Y		+
21293536-T-C	19131650-T-C		FT339032		Y	Y		+
21522917-C-A	19361031-C-A		FT339207		Y			+
21558165-G-A	19396279-G-A		FT339236		Y	Y		+
21572674-G-A	19410788-G-A		BY204180		Y	Y		+
22885015-A-G	20723129-A-G		FT339947		Y	Y		+
23532314-G-A	21370428-G-A		FGC37302		Y	Y		+
28635109-A-T	26488962-A-T		FT340748					+
58877533-T-C	56713338-A-G							+
4537610-C-T	4669569-C-T							+
2795559-G-GTTT	2927518-G-GTTT						24×T	+
2809558-TG-T	2941517-TG-T							+
2926312-A-G	3058271-A-G							+
3382165-T-C	3514124-T-C							+
3804815-A-G	3936774-A-G	FT112743						+
3809136-A-ATTT	3941095-A-ATTT						31×T	+
3812710-C-A	3944669-C-A							+
3812716-G-A	3944675-G-A							+
4067508-C-CTT	4199467-C-CTT						29×T	+
4090300-G-T	4222259-G-T							+
4090302-A-C	4222261-A-C							+
4780657-C-T	4912616-C-T		FT321723					+
5631437-A-G	5763396-A-G							+
5845872-G-C	5977831-G-C							+
5892773-C-G	6024732-C-G							+
5962149-T-TATAC	6094108-T-TATAC							+
7601007-G-GA	7732966-G-GA							+
7832071-GTCTTTCTTTCTT-G	7964030-GTCTTTCTTTCTT-G						18×TCTT	+
8575984-T-TTTTG	8707943-T-TTTTG							+
8725796-CAA-C	8857755-CAA-C							+
13194518-T-C	11038842-T-C							+
13213825-GGAT-G	11058149-GGAT-G							+
13213832-TGGA-T	11058156-TGGA-T							+
13257678-G-A	11102002-G-A							+
13280712-G-A	11125036-G-A		FT442253					+
13394853-C-G	11239177-C-G							+
13472425-C-T	11316749-C-T							+
13472439-G-T	11316763-G-T							+
13606877-C-CAA	11451201-C-CAA						25×A	+
13940855-GAA-G	11820149-GAA-G							+
13965291-G-A	11844585-G-A				Y			+
15305889-AG-A	13193991-AG-A							+
15315335-T-G	13203440-T-G		M5674		Y	Y		+
15981760-C-G	13869880-C-G				Y	Y		+
17109140-ACC-A	14997260-ACC-A							+
17998060-G-GT	15886180-G-GT			P7_Gap				+
18615932-C-CTTTTT	16504052-C-CTTTTT						27×T	+
18723887-C-T	16612007-C-T				Y	Y	19×T	+
21224778-GAT-G	19062892-GAT-G							+
21409460-C-CAAAA	19247574-C-CAAAA						30×A	+
21714727-A-C	19552841-A-C				Y	Y		+
21737341-A-C	19575455-A-C				Y	Y		+
21824255-C-CAAA	19662369-C-CAAA						30×A	+
22519781-A-G	20357895-A-G		FT339701		Y			+
22893304-CCTTTCTTTCTTTCTTT-C	20731418-CCTTTCTTTCTTTCTTT-C						17×CTTT	+
23899790-A-G	21737904-A-G							+
24600507-T-C	22454360-T-C			P3_t2				+
28797878-G-A	26651731-G-A							+
28797880-G-A	26651733-G-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:

Kit	POSITION-REF-ALT (hg19)	POSITION-REF-ALT (hg38)	Note
HG01953	16264788-T-A	14152908-T-A	No reads.
HG01953	22232902-C-A	20071016-C-A	Checked BAM File.
HG01953	9333959-G-A	9496350-G-A	Checked BAM File.
HG01953	13824242-G-T	11703536-G-T	Checked BAM File.
Manual	16264788-T-A	14152908-T-A	No Coverage.
Manual	19996272-C-T	17884392-C-T	6 reads with a T, 2 with a C.
Manual	22232902-C-A	20071016-C-A	9 reads total -- 5 with an A, 4 with a C.
Manual	24587965-T-C	22441818-T-C	2 reads with a T, one with a C. The read with a C has an additional mismatch relative to the reference sequence.
Manual	9333959-G-A	9496350-G-A	20 well aligned reads, 4 of which are A, and the balance G.
Manual	4439911-TGCAGCTTCACTCCTGAGG-T	4571870-TGCAGCTTCACTCCTGAGG-T	4 reads, all positive.
Manual	24077897-A-C	21931750-A-C	Negative. 10 reads, all A.
Manual	22300661-C-G	20138775-C-G	7G 3C
Manual	59027545-G-A	56881398-G-A	7A 1G for the reads with the highest mapping quality. Those with lower quality look to be misaligned.
Manual	24673173-G-GCACA	22527026-G-GCACA	2 reads. Both show the insertion.
Manual	3447135-T-C	3579094-T-C	1C 1T. The 1T may be misaligned.
Manual	5033066-T-C	5165025-T-C	3C 3T. The 3T reads has 0 mapping quality.
Manual	20962225-C-G	18800339-C-G	3C 4G. Only two of the reads have mapping quality > 0 and both are G.
Manual	22265352-G-T	20103466-G-T	3G 5T
Manual	24387249-CTATATATATCCCA-C	22241102-CTATATATATCCCA-C	Just one read, but it has the deletion.
Manual	25882430-A-G	23736283-A-G	2A 2G

1k Genomes

Tree Position

Unique Mutations

Mutation Notes: