Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > ZZ10 > Z253 > BY23615

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 STRBigY3
6358580-A-C 6490539-A-C A+
20084471-T-TTTC 17972591-T-TTTC P5_Dst A*
20424354-C-T 18262468-C-T P5_Dst A*
20420108-A-G 18258222-A-G P5_Dst A*
20392020-T-C 18230134-T-C P5_Dst A*
20386357-G-GT 18224471-G-GT P5_Dst A*
20290384-A-AT 18128498-A-AT P5_Dst A*
20271945-C-A 18110059-C-A P5_Dst A*
20265512-G-T 18103626-G-T P5_Dst A*
20259327-G-C 18097441-G-C P5_Dst A*
20228388-A-G 18066502-A-G P5_Dst A*
20213213-T-C 18051327-T-C P5_Dst A*
20045269-A-AAAG 17933389-A-AAAG P5_Prx A*
20472472-C-A 18310586-C-A P5_Dst A*
19939884-G-C 17828004-G-C P5_Prx A*
19773458-G-A 17661578-G-A P5_Prx A*
19667697-C-T 17555817-C-T P5_Prx A*
18489684-C-A 16377804-C-A P6_Dst A*
18439826-G-A 16327946-G-A P6_Dst A*
18009786-A-T 15897906-A-T P7_Dst YA*
13135213-T-C 10624699-T-C A*
13135241-T-C 10624727-T-C A*
16165971-A-G 14054091-A-G P8_Dst A*
16145549-A-G 14033669-A-G P8_Dst A*
26048742-C-A 23902595-C-A ZS3791 P1_Y1 A*
20467718-G-A 18305832-G-A P5_Dst A*
28785146-G-A 26638999-G-A A*
20481597-G-A 18319711-G-A P5_Dst A*
20944328-T-G 18782442-T-G P4_Dst A*
26145155-G-A 23999008-G-A P1_Y1 A*
24293639-C-T 22147492-C-T P3_t1 A*
23267695-G-GA 21105809-G-GA 11×AA*
20567757-A-G 18405871-A-G P5_Dst A*
20999497-T-C 18837611-T-C P4_Dst YA*
20983957-G-T 18822071-G-T P4_Dst A*
20966294-C-A 18804408-C-A P4_Dst A*
20950797-G-A 18788911-G-A P4_Dst A*
20945724-C-A 18783838-C-A P4_Dst A*
20244953-A-C 18083067-A-C P5_Dst A*
20894074-G-A 18732188-G-A P4_Dst A*
20594016-G-A 18432130-G-A P5_Dst A*
20885968-A-G 18724082-A-G P4_Dst A*
20603302-C-T 18441416-C-T P5_Dst A*
20594008-A-T 18432122-A-T P5_Dst A*
20606170-A-G 18444284-A-G P5_Dst A*
20690840-T-A 18528954-T-A P4_Prx A*
20848879-G-C 18686993-G-C P4_Dst A*
20859175-G-T 18697289-G-T P4_Dst A*
20859400-G-T 18697514-G-T P4_Dst A*
13231227-A-G 11075551-A-G BY204990 +
13657928-A-G 11502252-A-G BY210679 +
13661068-C-G 11505392-C-G BY210705 +
10948030-C-T +
13945448-C-T 11824742-C-T YY+
14232652-TTTC-T 12111946-TTTC-T +
14243085-G-T 12122379-G-T BY203110 YY+
10617366-G-A FT69742 +
14264335-A-G 12143629-A-G BY203115 YY+
15320753-C-T 13208871-C-T FT32482 YY+
24356932-T-G 22210785-T-G BY204608 +
16796903-T-C 14685023-T-C BY203511 YY+
16298433-G-T 14186553-G-T FT56545 YY+
16424974-C-T 14313094-C-T FT32544 Y+
16670523-A-G 14558643-A-G BY203492 YY+
23578082-T-C 21416196-T-C BY204540 YY+
16946807-A-G 14834927-A-G BY203549 YY+
22713783-C-T 20551897-C-T FT32780 Y+
18086338-G-A 15974458-G-A FT32635 Y+
18850609-A-C 16738729-A-C FT32678 YY+
18940534-T-A 16828654-T-A BY203920 YY+
19108058-C-T 16996178-C-T BY203957 YY+
19483884-C-A 17372004-C-A BY204047 Y+
9933930-G-A 10096321-G-A FT69743 Y+
22474766-C-G 20312880-C-G BY223214 DYZ19 +
15635-G-C +
7610315-C-T 7742274-C-T FT32291 YY+
3937871-T-C 4069830-T-C FT32010 +
22459825-C-T 20297939-C-T BY220402 DYZ19 +
5343414-T-A 5475373-T-A FGC40241 +
6412407-T-G 6544366-T-G FT32235 +
2947689-G-A 3079648-G-A FT31928 +
3269334-A-T 3401293-A-T FT31956 +
14362040-C-T 12241335-C-T Y66565 YY+
3891910-A-T 4023869-A-T FT32004 +
22280761-C-A 20118875-C-A DYZ19 *
22254080-C-G 20092194-C-G DYZ19 *
5041260-C-T 5173219-C-T *
13478583-T-C,G 11322907-T-C,G *
10693414-T-C *
5393736-GTA-G 5525695-GTA-G *
5393784-C-CTT 5525743-C-CTT 8×T*
14379598-GATAC-G 12258894-GATAC-G *
5041301-C-A 5173260-C-A FGC80989 *
5046565-T-C 5178524-T-C *
3662943-G-A 3794902-G-A FT44784 *
5087118-T-C 5219077-T-C A13019 *
13222723-GTACA-G 11067047-GTACA-G **
13453346-T-TGAC 11297670-T-TGAC **
13453378-C-CCCCTG 11297702-C-CCCCTG **
21823510-A-C 19661624-A-C **
13453365-A-G 11297689-A-G BY85372 **
21823505-G-A 19661619-G-A **
21823508-A-G 19661622-A-G **
7269588-ACTTT-A 7401547-ACTTT-A 5×CTTT**
21823519-C-T 19661633-C-T **
22236993-A-G 20075107-A-G DYZ19 **
23081972-A-G 20920086-A-G **
7016147-CA-C 7148106-CA-C 16×A**
11657353-G-A FT69744 **
13718426-G-C 11562750-G-C **
13482639-T-TC 11326963-T-TC **
18325660-G-T 16213780-G-T P6_Prx **
13482650-G-C 11326974-G-C **
13347384-A-G 11191708-A-G **
13496526-A-G 11340850-A-G **
3490581-C-T 3622540-C-T **
13214289-AT-A 11058613-AT-A 19×T***
4636092-T-TAA 4768051-T-TAA 15×A***
21084483-T-C 18922597-T-C ***
21120339-TA-T,TAA 18958453-TA-T,TAA 16×A***
7431131-T-C 7563090-T-C ***
16027301-T-TA 13915421-T-TA 8×A***
13488478-G-A 11332802-G-A ***
21915587-T-A 19753701-T-A ***
4375912-G-A 4507871-G-A ***
13195029-C-A 11039353-C-A ***
13530079-CAAA-C,CA 11374403-CAAA-C,CA 24×A***
3102417-A-AT 3234376-A-AT 17×T***
22972772-G-T 20810886-G-T ***
23019415-TGC-T 20857529-TGC-T ***
23029477-A-T 20867591-A-T ***
14783433-C-T 12671503-C-T CTS3270 ***
17733553-T-TAATA 15621673-T-TAATA 11×AATA***
24389894-CTTT-C,CTT 22243747-CTTT-C,CTT 26×T***
5041234-A-G 5173193-A-G ***
5828966-AACAC-A,AAC 5960925-AACAC-A,AAC 22×AC***
26456620-C-A 24310473-C-A P1_Y1 ***
26456623-A-T 24310476-A-T P1_Y1 ***
26456630-G-C 24310483-G-C P1_Y1 ***
5041572-A-G 5173531-A-G ***
7431164-A-C 7563123-A-C CTS1477 ***
5056960-G-T 5188919-G-T ***
14492793-CTT-C 12380990-CTT-C 15×T***
13463314-A-T 11307638-A-T ***
19271315-T-TA 17159435-T-TA ***
9136669-TTATA-T,TTA 9299060-TTATA-T,TTA 11×TA***
19203947-A-G 17092067-A-G ***
28461722-CT-C,CTT 26315575-CT-C,CTT 19×T***
13457953-C-G 11302277-C-G ***
6080268-C-CA 6212227-C-CA 10×A***
10781676-A-AATTCCATTCC ***
13457924-T-G 11302248-T-G ***
10647774-A-C ***
10961386-C-A ***
13457938-T-G 11302262-T-G ***
4213860-ATG-A 4345819-ATG-A 12×TG***
6024601-CAT-C 6156560-CAT-C ***
15324319-CTTTTT-C 13212437-CTTTTT-C 25×T***
15109457-A-AT 12997544-A-AT 14×T***
13457948-T-A 11302272-T-A 5×TCCAC***
17056769-C-T 14944889-C-T ***
13464535-C-A 11308859-C-A ***
13457958-C-A 11302282-C-A ***
3391605-C-CA 3523564-C-CA 11×A***
13135209-T-A 10624695-T-A ***
13457940-C-G 11302264-C-G ***
13135214-G-A 10624700-G-A ***
13464554-C-T 11308878-C-T BY210284 ***
22669081-T-A 20507195-T-A YFS3395655 ***
14667841-C-A 12555907-C-A ***
21238646-A-C 19076760-A-C ***

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.

Age Analysis Information (work in progress)

Kit: 7495321506760294522948346261
Used in age calculations1506760294522948346261
Counts of SNPs2114
Variant counts last updated 2019-07-19 22:58:52.

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