Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF49/S474 > Z2980 > Z2976 > DF23 > Z2961 > M222 > DF106 > DF104 > DF105 > DF85 > S673 > S668 > DF97 > ZZ36 > FGC19851 > Z29319 > BY35773 > BY21154 > BY21160 > 7894130-G-A

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
NA20318
Manual
Edits
22238328-C-T 20076442-C-T DYZ19 +
13428972-G-A 11273296-G-A +
13379355-A-G 11223679-A-G +
13379846-T-A 11224170-T-A +
13380306-T-C 11224630-T-C +
13415445-C-T 11259769-C-T +
13415463-C-T 11259787-C-T +
13415469-T-C 11259793-T-C +
13503705-A-G 11348029-A-G +
13362309-G-A 11206633-G-A +
13507005-C-T 11351329-C-T +
13571355-C-G 11415679-C-G +
13741495-G-C 11585819-G-C +
13885847-C-CTTTTT 11765141-C-CTTTTT +
13906194-A-C 11785488-A-C Y+
14083984-A-AGATT 11963278-A-AGATT +
14083998-A-ATAGG 11963292-A-ATAGG +
13362642-G-A 11206966-G-A +
13346776-C-CAA 11191100-C-CAA 13×A+
14645424-TG-T 12533488-TG-T +
13213845-GGAT-G 11058169-GGAT-G +
8232960-A-T 8364919-A-T YY+
8232960-AAGCAGTTAT-A 8364919-AAGCAGTTAT-A +
9063235-A-C 9225626-A-C Z12147 Y+
9939159-G-A 10101550-G-A Y+
9997125-TA-T 10159516-TA-T +
9998237-G-A 10160628-G-A Y+
13213848-TGGA-T 11058172-TGGA-T +
13308969-T-C 11153293-T-C +
13243848-T-C 11088172-T-C +
13254614-TC-T 11098938-TC-T +
13275764-T-G 11120088-T-G +
13275788-G-A 11120112-G-A +
13287957-A-ATT 11132281-A-ATT +
13287973-A-C 11132297-A-C +
13287975-A-C 11132299-A-C +
14083999-T-TAGAG 11963293-T-TAGAG +
14989218-T-TAAAAAA 12877284-TAAAAAAAAAAAAA-T 27×A+
8085515-TC-T 8217474-TC-T +
28644031-T-G 26497884-T-G +
27453877-T-C 25307730-T-C P1_Y2 +
27699914-T-A 25553767-T-A P1_Y2 +
28534932-A-AT 26388785-A-AT +
28534936-G-GT 26388789-G-GT +
28538802-G-C 26392655-G-C +
28569337-A-C 26423190-A-C +
28644043-C-T 26497896-C-T +
22269114-T-C 20107228-T-C DYZ19 +
28680560-G-A 26534413-G-A CTS12715 +
28726259-A-G 26580112-A-G Y+
28814566-A-T 26668419-A-T +
58867724-C-T 56723147-G-A +
58889745-T-C 56701126-A-G +
58895258-T-C 56695613-A-G +
58909665-C-T 56681206-G-A +
22325187-AAG-A 20163301-AAG-A DYZ19 +
22261446-A-G 20099560-A-G DYZ19 +
15271046-TG-T 13159135-TG-T +
19305551-G-GC 17193671-G-GC +
15660923-T-G 13549043-T-G YY+
16618905-T-C 14507025-T-C M5936 Y+
16757037-A-G 14645157-A-G YY+
17304010-T-G 15192130-T-G YY+
17867915-TC-T 15756035-TC-T +
17998060-G-GT 15886180-G-GT P7_Gap +
19305556-G-GT 17193676-G-GT +
22261440-T-C 20099554-T-C DYZ19 +
21403169-A-C 19241283-A-C YY+
21761933-T-G 19600047-T-G S23514 YY+
21823564-C-G 19661678-C-G Y12×G+
22048245-AT-A 19886359-AT-A +
22048297-T-A 19886411-T-A Y2660 FGC8094 B28 YY+
22048523-C-A 19886637-C-A YY13×A+
22198804-T-G 20036918-T-G YY+
8184331-CACTCTGAATGTTATAAA-C 8316290-CACTCTGAATGTTATAAA-C +
7511009-A-C 7642968-A-C Y+
9974223-T-TC 10136614-T-TC +
15909432-C-T 13797552-C-T Z25881 YY+
16583392-G-A 14471512-G-A YY10×A+
23113254-C-T 20951368-C-T YY+
2858966-A-G 2990925-A-G YY+
6674314-G-T 6806273-G-T YY+
7396516-G-A 7528475-G-A YY+
15796696-T-A 13684816-T-A Y+
17809281-C-T 15697401-C-T ZS5971 Z27696 YY+
28726230-T-G 26580083-T-G Y+
21572246-C-A 19410360-C-A YY+
22766234-G-A 20604348-G-A CTS10770 Y+
28498866-T-TA 26352719-T-TA 13×A+
28533050-C-T 26386903-C-T +
28693850-A-G 26547703-A-G +
22766233-CGTT-C 20604347-CGTT-C +
17998979-G-A 15887099-G-A P7_Gap Y+
14529234-C-A 12417435-C-A YY15×A+
22715168-G-A 20553282-G-A YY+
58839518-G-T 56751353-C-A +
13143957-N-C 10633443-N-C +
7568123-C-A 7700082-C-A YY10×A+
28755163-C-T 26609016-C-T CTS12938 Y+
13143253-T-C 10632739-T-C +
13306346-T-G 11150670-T-G +
17196590-G-A 15084710-G-A YY+
58891545-T-A 56699326-A-T +
13143958-N-T 10633444-N-T +
8184344-A-G 8316303-A-G YY+
13346771-A-C 11191095-A-C +
22294838-A-G 20132952-A-G DYZ19 +
4270959-AAGATAGATAGAT-A 4402918-AAGATAGATAGAT-A 15×AGAT+
22294800-G-C 20132914-G-C DYZ19 +
22300858-G-A 20138972-G-A DYZ19 +
22300856-A-T 20138970-A-T DYZ19 +
58842583-G-C 56748288-C-G +
13864564-CGGAATGGAAT-C 11743858-CGGAATGGAAT-C 12×GGAAT+
13747514-T-A 11591838-T-A +
7301697-T-G 7433656-T-G YY+
5540423-G-A 5672382-G-A +
4328388-T-G 4460347-T-G +
4328714-A-G 4460673-A-G +
4424365-G-GTT 4556324-G-GTT +
4487061-C-A 4619020-C-A +
4489035-A-G 4620994-A-G FGC76628 +
5268741-G-A 5400700-G-A +
5870015-A-G 6001974-A-G +
4002285-C-T 4134244-C-T +
5908086-A-G 6040045-A-G +
5941749-A-T 6073708-A-T ZS49 +
6855355-C-T 6987314-C-T YY+
6948092-G-GTTT 7080051-G-GTTT 31×T+
7028144-G-C 7160103-G-C Y+
7053358-AAAAGAAAGAAAGAAAGAAAG-A 7185317-AAAAGAAAGAAAGAAAGAAAG-A 17×AAAG+
7224621-T-G 7356580-T-G YY+
4136700-TCA-T 4268659-TCA-T 8×CA+
3755416-C-T 3887375-C-T +
13747547-A-T 11591871-A-T +
13686909-ACAC-A 11531233-ACAC-A +
6405591-T-G 6537550-T-G +
6405526-G-A 6537485-G-A +
13694756-G-GGAACT 11539080-G-GGAACT +
24447150-A-AGAAG 22301003-A-AGAAG 4×AAAG+
14467033-ATCTG-A 12346302-ATCTG-A +
5400487-TG-T 5532446-TG-T +
3851279-AGT-A 3983238-AGT-A 9×GT+
13641262-C-T 11485586-C-T +
3641043-TCTC-T 3773002-TCTC-T +
13641268-T-C 11485592-T-C +
14600814-T-TAC 12489014-T-TAC +
2856782-C-CTTTT 2988741-C-CTTTT 24×T+
2955378-CAT-C 3087337-CAT-C 9×AT+
2968166-G-A 3100125-G-A 13×A+
3185978-G-A 3317937-G-A +
3194426-C-G 3326385-C-G +
59019548-ACACAAG-A 56873401-ACACAAG-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
Manual2805834-C-T2937793-C-T2 reads, both T.
Manual22631679-G-A20469793-G-A4 reads, all A.
Manual25207083-G-A23060936-G-A3 reads. 2 are A and one is G.
Manual22766233-CGTT-C20604347-CGTT-C3 reads, all showing the missing GTT. There are two repeats of GTT at this location.
Manual22766234-G-A20604348-G-AChecking the BAM file, this doesn't look to be right. Instead, there is a deletion here, 22766233-CGTT-C.
Manual9386687-G-A9549078-G-A9 reads, 8 of which are A, the other is misaligned.
Manual22364704-A-G20202818-A-G2 reads with A, 2 reads with G. The two reads with G also have a pattern of other mutations which makes them looks as though they don't belong here. I'm not sure if the results for Reed (198419) are similar.
Manual10081968-C-G10244359-C-G5G
Manual4439911-TGCAGCTTCACTCCTGAGG-T4571870-TGCAGCTTCACTCCTGAGG-TJust one possible read, it's positive.
Manual22317690-G-A20155804-G-A2G 4A
Manual22317691-T-A20155805-T-A2T 4A



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