Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > ZZ10 > MC14 > BY246 > BY248 > A5383

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 STRFTDNA
14747500-C-A 12635569-C-A YY*
14365718-G-C 12245013-G-C YY*
23316265-C-T 21154379-C-T CTS11853 PF6227 YY*
16060868-C-A 13948988-C-A YY*
19543393-C-A 17431513-C-A YY*
6753447-C-T 6885406-C-T L229 YY*
6753459-G-T 6885418-G-T L393 M8966 Z4836 YY*
15025240-A-C 12913328-A-C YY*
15271994-C-T 13160083-C-T YY*
14487023-A-T 12366292-A-T **
13858249-C-T 11737543-C-T **
18255046-A-G 16143166-A-G PR2813 **
16607082-C-G 14495202-C-G **
13653148-A-T 11497472-A-T **
21554468-A-C 19392582-A-C **
15055079-A-G 12943170-A-G **
22767315-C-A 20605429-C-A **
7161607-G-C 7293566-G-C **
6859138-A-C 6991097-A-C **
6753937-G-T 6885896-G-T **
19271440-C-G 17159560-C-G PF7193 **
16282193-C-A 14170313-C-A **
15157840-G-T 13045927-G-T **
25458706-G-GA 23312559-G-GA P2_r2 9×A***
17781569-A-T 15669689-A-T ZS10038 ***
8702809-TG-T 8834768-TG-T ***
18952261-T-G 16840381-T-G ***
18509775-T-A 16397895-T-A P6_Dst ***
18454721-T-A 16342841-T-A P6_Dst ***
18297500-CATAA-C 16185620-CATAA-C P6_Prx ***
24731827-AT-A 22585680-AT-A P3_b2 9×T***
18125696-C-G 16013816-C-G ***
17861975-A-G 15750095-A-G ***
17781588-C-T 15669708-C-T ***
17781577-A-T 15669697-A-T ***
27714328-CTT-C 25568181-CTT-C P1_Y2 15×T***
17781568-T-A 15669688-T-A ***
20012744-A-AGT 17900864-A-AGT P5_Prx ***
17781489-T-A 15669609-T-A ***
17413954-G-C 15302074-G-C ***
17337165-C-T 15225285-C-T CTS7177 ***
13845541-A-AAATGG 11724835-A-AAATGG 8×AATGG***
17319876-A-G 15207996-A-G ***
17039327-G-A 14927447-G-A F2364 AM00682 ***
13253951-C-A,G 11098275-C-A,G ***
16345432-A-AG 14233552-A-AG ***
13453279-AGTTTG-A,C 11297603-AGTTTG-A,C ***
13484085-T-A,C 11328409-T-A,C ***
7494067-AG-A 7626026-AG-A IR1_L ***
20040567-AGAAG-A 17928687-AGAAG-A P5_Prx 4×GAAG***
25106467-C-A 22960320-C-A g1 ***
27008924-GCA-G 24862777-GCA-G P1_r4 ***
26112445-A-G 23966298-A-G P1_Y1 ***
26170490-A-C 24024343-A-C P1_Y1 ***
26216077-A-AGT 24069930-A-AGT P1_Y1 ***
25096813-AGAG-A 22950666-AGAG-A g1 ***
26880170-C-A 24734023-C-A P1_r3 ***
25014710-GACCAT-G 22868563-GACCAT-G g1 ***
24847892-ACTAATTCCCT-A 22701745-ACTAATTCCCT-A IR1_R ***
24812531-AT-A 22666384-AT-A P3_b2 10×T***
24805977-T-C 22659830-T-C P3_b2 ***
24749756-GGGGAGC-T 22603609-GGGGAGC-T P3_b2 ***
24728630-T-C 22582483-T-C P3_b2 ***
27781145-AT-A 25634998-AT-A P1_Y2 10×T***
20360957-AT-A 18199071-AT-A P5_Dst 10×T***
22460218-C-A 20298332-C-A DYZ19 ***
22427337-C-G 20265451-C-G DYZ19 ***
27800870-G-C 25654723-G-C P1_Y2 ***
22427330-GTTTGT-C 20265444-GTTTGT-C DYZ19 ***
22340930-G-A 20179044-G-A DYZ19 ***
22293056-C-A 20131170-C-A DYZ19 ***
22292689-A-T 20130803-A-T DYZ19 ***
58826879-G-C 56763992-C-G 4×CATTC***
20969634-A-G 18807748-A-G P4_Dst ***
58974773-G-T 56828626-G-T ***
20796645-AT-A 18634759-AT-A P4_Prx 10×T***
20659122-CTGAG-T 18497236-CTGAG-T P4_Prx ***
22427336-T-C 20265450-T-C DYZ19 ***
16292546-A-ATTT 14180666-A-ATTT 48×T***
15420840-TAC-T 13308960-TAC-T ***
15092687-G-C 12980776-G-C ***
9989400-G-T 10151791-G-T PR4938 ***
9968221-C-T 10130612-C-T ***
9959618-A-C 10122009-A-C ***
9943151-C-G 10105542-C-G ***
9312256-T-G 9474647-T-G ***
8411202-GA-T 8543161-GA-T ***
7660672-G-T 7792631-G-T FGC39907 ***
7473844-AGAG-A 7605803-AGAG-A IR1_L ***
7224638-C-T 7356597-C-T CTS1127 ***
6947396-C-T 7079355-C-T ***
6233108-C-A 6365067-C-A IR3_Dst ***
28802898-A-AG 26656751-A-AG ***
22340946-C-T 20179060-C-T PF1153 DYZ19 ***
22340942-A-T 20179056-A-T DYZ19 ***
13860153-T-A 11739447-T-A ***
9989435-T-A 10151826-T-A ***
20937050-AT-A 18775164-AT-A P4_Dst 14×T***
15538288-A-AG 13426408-A-AG ***
22291024-A-G 20129138-A-G DYZ19 ***
13542959-AC-A 11387283-AC-A ***
13805318-T-A 11684612-T-A ***
15471963-T-A 13360083-T-A ***
15471973-T-C 13360093-T-C ***
13716714-A-T 11561038-A-T ***
13664378-G-C 11508702-G-C ***
13858654-G-C 11737948-G-C ***
22291034-G-T 20129148-G-T DYZ19 ***
26204066-C-T 24057919-C-T P1_Y1 ***
27785784-TA-T 25639637-TA-T P1_Y2 10×A***
19261335-TGA-T 17149455-TGA-T 8×GA***
9989419-T-C 10151810-T-C ***
9989449-C-T 10151840-C-T PR4940 ***
13735865-T-G 11580189-T-G ***
14937963-G-A 12826038-G-A ***
22420181-C-T 20258295-C-T DYZ19 ***
14606044-G-T 12494246-G-T ***
14529537-C-A 12417738-C-A ***
14319328-C-T 12198622-C-T CTS2469 ***
13960962-G-T 11840256-G-T ***
13869643-C-G,T 11748937-C-G,T ***
13857526-G-T 11736820-G-T ***
13852671-A-G 11731965-A-G ***
13820745-A-G 11700039-A-G ***
13802960-A-C 11682254-A-C ***
13802953-A-C 11682247-A-C ***
13802922-TGGAAG-T 11682216-TGGAAG-T ***
10019404-G-A 10181795-G-A ***
13676277-G-A 11520601-G-A ***
13451706-T-C 11296030-T-C ***
13455171-G-A 11299495-G-A ***
13542887-G-A 11387211-G-A ***
13639633-A-G 11483957-A-G ***
13652070-G-T 11496394-G-T ***
13676272-C-T 11520596-C-T BY210859 ***
13680793-A-T 11525117-A-T ***
13723383-A-T 11567707-A-T ***
13680805-G-A 11525129-G-A ***
13689140-A-G 11533464-A-G BY88546 ***
13691313-GGAAAGATATC-G 11535637-GGAAAGATATC-G ***
13703544-A-T 11547868-A-T BY211146 ***
13703621-C-G 11547945-C-G FT449040 ***
13715827-G-A 11560151-G-A ZS9159 F14761 ***

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:

Manual17306210-GA-G15194330-GA-G12 reads with the deletion, many of which look to be duplicates.

Age Analysis Information (work in progress)

Kit: N49035979014669630227009473
Used in age calculations979014669630227009473
Counts of SNPs99
Variant counts last updated 2021-11-24 04:03:12.

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