Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > S1051 > ~19996272-C-T > FGC14899 > Y125244

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
HG01953
Manual
Edits
20995546-TCTTTC-T 18833660-TCTTTC-T P4_Dst 11×CTTTC+
8725796-CAA-C 8857755-CAA-C +
13472425-C-T 11316749-C-T +
13394853-C-G 11239177-C-G +
13280712-G-A 11125036-G-A FT442253 +
13257678-G-A 11102002-G-A +
13213832-TGGA-T 11058156-TGGA-T +
13213825-GGAT-G 11058149-GGAT-G +
13194518-T-C 11038842-T-C +
8575984-T-TTTTG 8707943-T-TTTTG +
13606877-C-CAA 11451201-C-CAA 25×A+
7832071-GTCTTTCTTTCTT-G 7964030-GTCTTTCTTTCTT-G 18×TCTT+
7601007-G-GA 7732966-G-GA +
5962149-T-TATAC 6094108-T-TATAC +
5892773-C-G 6024732-C-G +
5845872-G-C 5977831-G-C +
5631437-A-G 5763396-A-G +
4780657-C-T 4912616-C-T FT321723 +
13472439-G-T 11316763-G-T +
13940855-GAA-G 11820149-GAA-G +
4090300-G-T 4222259-G-T +
21714727-A-C 19552841-A-C YY+
28797878-G-A 26651731-G-A +
24600507-T-C 22454360-T-C P3_t2 +
23899790-A-G 21737904-A-G +
22893304-CCTTTCTTTCTTTCTTT-C 20731418-CCTTTCTTTCTTTCTTT-C 17×CTTT+
22519781-A-G 20357895-A-G FT339701 Y+
21824255-C-CAAA 19662369-C-CAAA 30×A+
21737341-A-C 19575455-A-C YY+
21409460-C-CAAAA 19247574-C-CAAAA 30×A+
13965291-G-A 11844585-G-A Y+
21224778-GAT-G 19062892-GAT-G +
18723887-C-T 16612007-C-T YY19×T+
18615932-C-CTTTTT 16504052-C-CTTTTT 27×T+
17998060-G-GT 15886180-G-GT P7_Gap +
17109140-ACC-A 14997260-ACC-A +
15981760-C-G 13869880-C-G YY+
15315335-T-G 13203440-T-G M5674 YY+
15305889-AG-A 13193991-AG-A +
4090302-A-C 4222261-A-C +
4067508-C-CTT 4199467-C-CTT 29×T+
3570961-C-A 3702920-C-A +
8589495-A-G 8721454-A-G Z13358 YY+
16767285-C-T 14655405-C-T FT337021 YY+
16549164-A-T 14437284-A-T FT336884 YY+
16486492-G-T 14374612-G-T FT336839 YY+
16037283-T-C 13925403-T-C FT336560 YY+
15942628-T-C 13830748-T-C FT336483 YY+
15002075-C-A 12890160-C-A FT335899 YY+
8863138-G-A 8995097-G-A FT334777 YY+
8424426-A-C 8556385-A-C FT334463 YY+
17390622-T-C 15278742-T-C FT337406 YY+
7788558-T-C 7920517-T-C FT334051 YY+
7750725-C-T 7882684-C-T FT334026 YY+
7560871-C-G 7692830-C-G FT333909 YY+
2861387-T-C 2993346-T-C FT333453 YY+
2748998-T-C 2880957-T-C FT333398 YY+
19346429-T-TCTTC 17234549-T-TCTTC +
58894781-G-A 56696090-C-T +
16999901-C-T 14888021-C-T FT337156 Y+
17519156-G-C 15407276-G-C FT337494 Y+
3812716-G-A 3944675-G-A +
4537610-C-T 4669569-C-T +
3812710-C-A 3944669-C-A +
3809136-A-ATTT 3941095-A-ATTT 31×T+
3804815-A-G 3936774-A-G +
3382165-T-C 3514124-T-C +
2926312-A-G 3058271-A-G +
2809558-TG-T 2941517-TG-T +
2795559-G-GTTT 2927518-G-GTTT 24×T+
58877533-T-C 56713338-A-G +
17939965-T-A 15828085-T-A FT337791 YY+
28635109-A-T 26488962-A-T FT340748 +
23532314-G-A 21370428-G-A FGC37302 YY+
22885015-A-G 20723129-A-G FT339947 YY+
21572674-G-A 19410788-G-A BY204180 YY+
21558165-G-A 19396279-G-A FT339236 YY+
21522917-C-A 19361031-C-A FT339207 Y+
21293536-T-C 19131650-T-C FT339032 YY+
19080228-T-C 16968348-T-C YY+
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
HG0195316264788-T-A14152908-T-ANo reads.
HG0195322232902-C-A20071016-C-AChecked BAM File.
HG019539333959-G-A9496350-G-AChecked BAM File.
HG0195313824242-G-T11703536-G-TChecked BAM File.
Manual16264788-T-A14152908-T-ANo Coverage.
Manual19996272-C-T17884392-C-T6 reads with a T, 2 with a C.
Manual22232902-C-A20071016-C-A9 reads total -- 5 with an A, 4 with a C.
Manual24587965-T-C22441818-T-C2 reads with a T, one with a C. The read with a C has an additional mismatch relative to the reference sequence.
Manual9333959-G-A9496350-G-A20 well aligned reads, 4 of which are A, and the balance G.
Manual4439911-TGCAGCTTCACTCCTGAGG-T4571870-TGCAGCTTCACTCCTGAGG-T4 reads, all positive.
Manual24077897-A-C21931750-A-CNegative. 10 reads, all A.
Manual22300661-C-G20138775-C-G7G 3C
Manual59027545-G-A56881398-G-A7A 1G for the reads with the highest mapping quality. Those with lower quality look to be misaligned.
Manual24673173-G-GCACA22527026-G-GCACA2 reads. Both show the insertion.
Manual3447135-T-C3579094-T-C1C 1T. The 1T may be misaligned.
Manual5033066-T-C5165025-T-C3C 3T. The 3T reads has 0 mapping quality.
Manual20962225-C-G18800339-C-G3C 4G. Only two of the reads have mapping quality > 0 and both are G.
Manual22265352-G-T20103466-G-T3G 5T
Manual24387249-CTATATATATCCCA-C22241102-CTATATATATCCCA-CJust one read, but it has the deletion.
Manual25882430-A-G23736283-A-G2A 2G



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